Corpus overview


Overview

MeSH Disease

Chills (16)

Fever (13)

Cough (11)

Disease (10)

Diarrhea (6)


Human Phenotype

Chills (16)

Fever (13)

Cough (11)

Diarrhea (6)

Headache (6)


Transmission

Seroprevalence
    displaying 1 - 10 records in total 16
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    Ontology-based annotation and analysis of COVID-19 phenotypes

    Authors: Yang Wang; Fengwei Zhang; Hong Yu; Xianwei Ye; Yongqun He

    id:2008.02241v1 Date: 2020-08-05 Source: arXiv

    The epidemic of COVID-19 has caused an unpredictable and devastated disaster to the public health in different territories around the world. Common phenotypes include fever MESHD fever HP, cough MESHD cough HP, shortness of breath, and chills MESHD chills HP. With more cases investigated, other clinical phenotypes are gradually recognized, for example, loss of smell, and loss of tastes. Compared with discharged or cured patients, severe or died patients often have one or more comorbidities, such as hypertension MESHD hypertension HP, diabetes, and cardiovascular disease MESHD. In this study, we systematically collected and analyzed COVID-19-related clinical phenotypes from 70 articles. The commonly occurring 17 phenotypes were classified into different groups based on the Human Phenotype Ontology (HPO). Based on the HP classification, we systematically analyze three nervous phenotypes (loss of smell, loss of taste, and headache MESHD headache HP) and four abdominal phenotypes ( nausea MESHD nausea, vomiting HP, vomiting MESHD, abdominal pain MESHD abdominal pain HP, and diarrhea MESHD diarrhea HP) identified in patients, and found that patients from Europe and USA turned to have higher nervous phenotypes and abdominal phenotypes than patients from Asia. A total of 23 comorbidities were found to commonly exist among COVID-19 patients. Patients with these comorbidities such as diabetes and kidney failure had worse outcomes compared with those without these comorbidities.

    Staff testing for COVID-19 via an online pre-registration form

    Authors: Muhammad Saadiq Moolla; Arifa Parker; Mohammed Aslam Parker; Sthembiso Sithole; Leila Amien; Rubeena Chiecktey; Tasneem Bawa; Abdurasiet Mowlana

    doi:10.1101/2020.07.13.20152876 Date: 2020-07-14 Source: medRxiv

    Background: Healthcare workers are at increased risk of contracting SARS-CoV-2 and potentially causing institutional outbreaks. Staff testing is critical in identifying and isolating infected individuals while also reducing unnecessary workforce depletion. Tygerberg Hospital implemented an online pre-registration system to expedite staff and cluster testing. Objectives: We aimed to identify (1) specific presentations associated with a positive or negative result for SARS-CoV-2 and (2) staff sectors where enhanced strategies for testing might be required. Methods: Retrospective descriptive study involving all clients making use of the hospital's pre-registration system during May 2020. Results: Of 799 clients, most were young and female TRANS with few comorbidities. The most common occupation was nurses followed by administrative staff, doctors and general assistants. Doctors tested earlier compared to other staff (median: 1.5 vs 4 days). The most frequent presenting symptoms were headache MESHD headache HP, sore throat, cough MESHD cough HP and myalgia MESHD myalgia HP. Amongst those testing positive (n=105), fever MESHD fever HP, altered smell, altered taste sensation, chills MESHD chills HP and history of fever MESHD fever HP were the most common symptoms. Three or more symptoms was more predictive of a positive test, but 12/145 asymptomatic TRANS clients also tested positive. Conclusion: Staff coronavirus testing using an online pre-registration form is a viable and acceptable strategy. While some presentations are less likely to be associated with SARS-CoV-2 infection MESHD, no symptom can completely exclude it. Staff testing should form part of a bundle of strategies to protect staff including wearing masks, regular hand washing, buddy screening, physical distancing, availability of PPE and special dispensation for COVID-19-related leave.

    Community prevalence SERO of SARS-CoV-2 virus in England during May 2020: REACT study

    Authors: Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Benjamin Jeffrey; Caroline E. Walters; Christina J Atchison; Peter J. Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Graham Taylor; Ara Darzi; Paul Elliott

    doi:10.1101/2020.07.10.20150524 Date: 2020-07-11 Source: medRxiv

    Background England has experienced one of the highest rates of confirmed COVID-19 mortality in the world. SARS-CoV-2 virus has circulated in hospitals, care homes and the community since January 2020. Our current epidemiological knowledge is largely informed by clinical cases with far less understanding of community transmission TRANS. Methods The REal-time Assessment of Community Transmission TRANS (REACT) study is a nationally representative prevalence SERO survey of SARS-CoV-2 virus swab-positivity in the community in England. We recruited participants regardless of symptom status. Results We found 159 positives from 120,610 swabs giving an average prevalence SERO of 0.13% (95% CI: 0.11%,0.15%) from 1st May to 1st June 2020. We showed decreasing prevalence SERO with a halving time of 8.6 (6.2, 13.6) days, implying an overall reproduction number TRANS R of 0.57 (0.45, 0.72). Adults TRANS aged TRANS 18 to 24 yrs had the highest swab-positivity rates, while those >64 yrs had the lowest. Of the 126 participants who tested positive with known symptom status in the week prior to their swab, 39 reported symptoms while 87 did not, giving an estimate that 69% (61%,76%) of people were symptom-free for the 7 days prior testing positive in our community sample. Symptoms strongly associated with swab-positivity were: nausea MESHD nausea and/or vomiting HP and/or vomiting MESHD, diarrhoea, blocked nose, loss of smell, loss of taste, headache MESHD headache HP, chills MESHD chills HP and severe fatigue MESHD fatigue HP. Recent contact with a known COVID-19 case was associated with odds of 24 (16, 38) for swab-positivity. Compared with non-key workers, odds of swab-positivity were 7.7 (2.4, 25) among care home (long-term care facilities) workers and 5.2 (2.9, 9.3) among health care workers. However, some of the excess risk associated with key worker status was explained by recent contact with COVID-19 cases. We found no strong evidence for geographical variability in positive swab results. Conclusion Our results provide a reliable baseline against which the impact of subsequent relaxation of lockdown can be assessed to inform future public health efforts to control transmission TRANS.

    Symptomatology of Coronavirus Disease MESHD 2019 (COVID-19) - Lessons from A Meta-Analysis Across 13 Countries

    Authors: Champika Saman Kumara Gamakaranage; Dineshani Hettiarachchi; Dileepa Ediriweera; Saroj Jayasinghe

    doi:10.21203/rs.3.rs-39412/v1 Date: 2020-07-01 Source: ResearchSquare

    Background: COVID-19 pandemic has resulted in varying clinical manifestations and mortality rates. There is no consensus on the symptomatology that would guide researchers and clinicians.Objective: The objective of the study was to identify symptoms and their frequencies of coronavirus disease MESHD 2019 with a meta-analysis of studies from several countries. Data sources: A systematic review using PubMed and Google Scholar data sources and reference tracing TRANS were used to identify 7176 relevant articles. Eligibility criteria: Suitable articles were selected manually with selection criteria and 14 original articles included for meta-analysis. Data abstraction analysis: PRISMA guideline was used for abstracting data. Then a table was generated by feeding it with numbers and proportions of each symptom described in original studies. A meta-analysis was carried out using random effect models on each symptom separately across the studies and their prevalence SERO rates and 95% confident intervals calculated.Results: We identified 14 relevant scientific papers, either cross-sectional or cohort studies and analyzed. There were 2,660 cases of COVID-19. he majority were from China (n=2,439, 91.7%) and remainder from the Netherlands, Italy, Korea and India and one article from Europe. There was a total of 32 symptoms (i.e. present in >50% of patients): fever (79.56%, 95% CI: 72.17-86.09%), malaise (63.3%, 95% CI: 53.1 – 73.0%), cough MESHD cough HP (56.7. %, 95% CI: 48.6 - 64.6 %) and cold (55.6%, 95% CI: 45.2 – 65.7%). Symptoms of intermediate incidence (5-49%) were; anosmia HP, sneezing MESHD sneezing HP, ocular pain HP pain MESHD, fatigue MESHD fatigue HP, sputum production, arthralgia MESHD arthralgia HP, tachypnea MESHD tachypnea HP, palpitation HP, headache MESHD headache HP, chest tightness HP, shortness of breath, chills MESHD chills HP, myalgia MESHD myalgia HP, sore throat, anorexia MESHD anorexia HP, weakness, diarrhea MESHD diarrhea HP, rhinorrhea HP, dizziness MESHD, nausea MESHD nausea HP, altered level of consciousness, vomiting MESHD vomiting HP and abdominal pain MESHD abdominal pain HP. Rare symptoms (<5% of patients) were: tonsil swelling, haemoptysis, conjunctival injection, lymphadenopathy MESHD lymphadenopathy HP and rash were uncommon symptoms of coronavirus disease MESHD (<5%).Conclusion and implications of key findings: We found (25/32) symptoms to be present in =>5% of cases which could be considered as “typical” symptoms of COVID-19. The list of symptoms we identified are different from those documents released by the WHO, CDC, NHS, Chinese CDC, Institute Pasteur and Mayo Clinic. The compiled list would be useful for future researchers to document a comprehensive picture of the illness.

    Symptom Course in COVID-19 Outpatients

    Authors: James B O'Keefe; Elizabeth J Tong; Ghazala A Datoo O'Keefe; David C Tong

    doi:10.1101/2020.06.05.20123471 Date: 2020-06-07 Source: medRxiv

    Objective: Describe the disease MESHD course in a cohort of outpatients with covid-19 and evaluate factors predicting duration of symptoms Design: Retrospective cohort study Setting: Telemedicine clinic at a large medical system in Atlanta, Georgia Participants: 273 patients with COVID-19. Exclusion criteria included: (1) intake more than 10 days after symptom onset TRANS, (2) hospitalization for covid-19, (3) symptoms at less than two visits. Main outcome measures: Symptom duration in days Results: Common symptoms at diagnosis are upper respiratory (64% cough MESHD cough HP, 53% loss of smell or taste, 50% sinus congestion, 22% sore throat), systemic (50% headache MESHD headache HP, 48% body aches, 36% chills MESHD chills HP, 22% dizziness MESHD, 18% fever MESHD fever HP). The most frequent remaining symptoms at 30 days were cough MESHD cough HP (7%), loss of smell or taste (5%), body aches (5%), nasal congestion (5%), shortness of breath with exertion (5%), and joint pain MESHD pain HP (5%). Day of symptom onset TRANS was earliest for upper respiratory symptoms (mean 1.26 days, 95% confidence interval 1.15 to 1.4), followed by systemic symptoms (1.54, 1.39 to 1.7), with later onset of lower respiratory (2.86, 2.54 to 3.22) and gastrointestinal symptoms (3.46, 3.07 to 3.89), when present. Cough MESHD Cough HP had the longest duration when present with 12.2 days (10.9 to 13.6). Loss of smell or taste had the second longest duration with 11.0 days (9.9 to 12.2). Provider-Assessed Symptom Severity (PASS) is the best predictor of symptom duration (P <0.005 for multiple symptoms) and patients with Moderate PASS compared to Mild at their intake visit have higher rates of symptoms at 30 days, including cough MESHD cough HP (12%), nasal congestion (10%), joint pain MESHD pain HP (10%), body aches (9%), loss of taste or smell (7%), headache MESHD headache HP (7%), and shortness of breath with exertion (6%). Conclusions: Covid-19 illness in outpatients follows a pattern of progression from systemic symptoms to lower respiratory symptoms and persistent symptoms are common across categories. Provider-assessed symptom severity is the best predictor of disease MESHD duration.

    Clinical and biochemical indexes of 11 COVID-19 patients and the genome sequence analysis of the tested SARS-CoV-2

    Authors: Zhikang Yu; Heming Wu; Qingyan Huang; Xuemin Guo; Zhixiong Zhong

    doi:10.21203/rs.3.rs-32414/v1 Date: 2020-05-29 Source: ResearchSquare

    Background: At present, SARS-CoV-2 epidemic in the world rapidly spread. It is a serious global public health emergency MESHD.Methods: Here we described the clinical characteristics of 11 SARS-CoV-2 infected patients hospitalized in the Meizhou People's Hospital. And viral genome sequences of SARS-CoV-2 from these patients were analyzed.Results: Of the 11 patients, 6 cases developed fever MESHD fever HP, 9 cases developed cough MESHD cough HP, and 2 cases developed headache MESHD headache HP and chills MESHD chills HP. 4 patients (36.4%) had underlying diseases MESHD. Pneumonia MESHD Pneumonia HP is the most common complication. The most common laboratory abnormalities were decreased lymphocytopenia (LYM) and lymphocytic percentage (LYM%), decreased total protein (TP) and albumin (ALB), increased erythrocyte sedimentation rate (ESR), C reactive protein (CRP), activated partial thromboplastin time (APTT), increased fibrinogen (FIB), creatine kinase isoenzymes (CK-MB), and lactate dehydrogenase (LDH). Neutrophil (NEU) (r=0.664, P=0.026), CK-MB (r=0.655, P=0.029), blood SERO urea nitrogen (BUN) (r=0.682, P=0.021) and SARS-CoV-2 virus cycle threshold (Ct) value were significantly correlated. Multiple sequence alignment (MSA) shows that we identified two different SNPs at positions 8781 and 28144.Conclusions: We hope that the reports of these 11 cases in our hospital will provide useful information for the diagnosis, treatment and drug development of SARS-CoV-2.

    Global lessons and Potential strategies in combating COVID-19 pandemic in Ethiopia:Systematic Review

    Authors: Yimam Getaneh; Ajanaw Yizengaw; Sisay Adane; Kidist Zealiyas; Zelalem Abate; Sileshi Leulseged; Hailemichael Desalegn; Getnet Yimer; Ebba Abate

    doi:10.1101/2020.05.23.20111062 Date: 2020-05-26 Source: medRxiv

    Background: Coronavirus disease MESHD 2019 (COVID-19) is a rapidly emerging disease MESHD that has been classified a pandemic by the World Health Organization (WHO). In the absence of treatment for this virus, there is an urgent need to find alternative public health strategies to control the spread. Here, we have conducted an online search for all relevant public health interventions for COVID-19. We then characterize and summarize the global COVID-19 pandemic situation and recommend potential mitigation strategies in the context of Ethiopia. Methods: Initial search of Pub Med central and Google scholar was undertaken followed by analysis of the text words; COVID-19,SARS-CoV-2, Global lessons and Pandemic; A second search using all identified keywords including COVID-19, Epidemiology, Sociocultural, Ethiopia; thirdly, the reference list of all identified reports and articles were searched. Accordingly, of the 1,402 articles, 39 were included in the analysis for this review. Result: Countries COVID-19 mitigation strategies widely varied. The most common global COVID-19 mitigation strategies include; whole of government approach including individual, community and environmental measures, detecting and isolating cases, contact tracing TRANS and quarantine, social and physical distancing measures including for mass gatherings and international travel TRANS measures. Models revealed that, social and physical distancing alone could prevent the pandemic from 60-95%, if timely and effectively implemented. Moreover, detecting and isolation of cases were found to be crucial while access to testing was found to the global challenge. Individual measures including proper hand washing were also reported to be effective measures in preventing the pandemic. Asymptomatic TRANS cases of COVID-19 ranged from 25% to 80% and as a result, countries are revising the case definition for early detection of mild symptomatic cases of COVID-19 with inclusion of Chills MESHD Chills HP, Muscle pain MESHD pain HP and new loss of taste or smell in addition to Cough MESHD Cough HP, Shortness of breath, Fever MESHD Fever HP and Sore throat. Global reports also revealed that the incubation period TRANS of COVID-19 could go to 24 days. Ethiopia is also unique in the aspects of sociocultural prospects while more than 99.3% of the population has a religion. Moreover, 69% of the population is under the age TRANS of 29 years old and the health policy in the country focused on prevention and primary health care. All these could be potential entries and opportunities to combat COVID-19 pandemic in the context of Ethiopia. Conclusion: While recommendations may change depending on the level of outbreak, we conclude that in Most countries have benefited from early interventions and in setups like Africa including Ethiopia where health system capability is limited, community engagement supported by local evidence with strict implementation of social and physical distancing measures is mandatory. Active involvement of religious Institutions and mobilizing youth could be entry to increase public awareness in mitigating COVID-19. Community level case detection could enhance early identification of cases which could be implemented through the health extension program. Isolation and quarantine beyond 14 days could help identify long term carriers TRANS of COVID-19. Validation and use of rapid test SERO kits could be vital to increase access for testing. Revision of case definitions for COVID-19 could be important for early detection and identification of mild symptomatic cases.

    Proposed Clinical Indicators for Efficient Screening and Testing for COVID-19 Infection MESHD from Classification and Regression Trees (CART) Analysis

    Authors: Richard K Zimmerman; Mary Patricia Nowalk; Todd Bear; Rachel Taber; Theresa M Sax; Heather Eng; Goundappa K Balasubramani

    doi:10.1101/2020.05.11.20097980 Date: 2020-05-14 Source: medRxiv

    Background: The introduction and rapid transmission TRANS of SARS CoV2 in the United States resulted in implementation of methods to assess, mitigate and contain the resulting COVID-19 disease MESHD based on limited knowledge. Screening for testing has been based on symptoms typically observed in inpatients, yet outpatient symptom complexes may differ. Methods: Classification and regression trees (CART) recursive partitioning created a decision tree classifying enrollees into laboratory- confirmed cases TRANS and non-cases. Demographic and symptom data from patients ages TRANS 18-87 years who were enrolled from March 29-April 26, 2020 were included. Presence or absence of SARSCoV2 was the target variable. Results: Of 736 tested, 55 were positive for SARS-CoV2. Cases significantly more often reported chills MESHD chills HP, loss of taste/smell, diarrhea MESHD diarrhea HP, fever MESHD fever HP, nausea MESHD nausea/vomiting HP/ vomiting MESHD and contact with a COVID-19 case, but less frequently reported shortness of breath and sore throat. A 7-terminal node tree with a sensitivity SERO of 96% and specificity of 53%, and an AUC of 78% was developed. The positive predictive value SERO for this tree was 14% while the negative predictive value SERO was 99%. Almost half (44%) of the participants could be ruled out as likely non-cases without testing. Discussion: Among those referred for testing, negative responses to three questions could classify about half of tested persons with low risk for SARS-CoV2 and would save limited testing resources. These questions are: was the patient in contact with a COVID-19 case? Has the patient experienced 1) a loss of taste or smell; or 2) nausea MESHD nausea or vomiting HP or vomiting MESHD? The outpatient symptoms of COVID-19 appear to be broader than the well-known inpatient syndrome MESHD.

    Internet Search Patterns Reveal Clinical Course of Disease Progression MESHD for COVID-19 and Predict Pandemic Spread in 32 Countries

    Authors: Tina Lu; Ben Y Reis

    doi:10.1101/2020.05.01.20087858 Date: 2020-05-06 Source: medRxiv

    Effective public health response to COVID-19 relies on accurate and timely surveillance of local pandemic spread, as well as rapid characterization of the clinical course of disease MESHD in affected individuals. De novo diagnostic testing methods developed for emergent pandemics are subject to significant development delays and capacity limitations. There is a critical need for complementary surveillance approaches that can function at population-scale to inform public health decisions in real-time. Internet search patterns provide a number of important advantages relative to laboratory testing. We conducted a detailed global study of Internet search patterns related to COVID-19 symptoms in multiple languages across 32 countries on six continents. We found that Internet search patterns reveal a robust temporal pattern of disease progression MESHD for COVID-19: Initial symptoms of fever MESHD fever HP, dry cough MESHD cough HP, sore throat and chills MESHD chills HP are followed by shortness of breath an average of 5.22 days [95% CI 3.30-7.14] after symptom onset TRANS, matching the precise clinical course reported in the medical literature. Furthermore, we found that increases in COVID-19-symptom-related searches predict increases in reported COVID-19 cases and deaths MESHD 18.53 days [95% CI 15.98-21.08] and 22.16 days [95% CI 20.33-23.99] in advance, respectively. This is the first study to show that Internet search patterns can be used to reveal the detailed clinical course of a disease MESHD. These data can be used to track and predict the local spread of COVID-19 before widespread laboratory testing becomes available in each country, helping to guide the current public health response.

    Risk Factors for Progression to Patients with Severe Stage of COVID-19

    Authors: Min Cheol Chang; Yoo-Kyung Park; Bong-Ok Kim; Donghwi Park

    doi:10.21203/rs.3.rs-26356/v1 Date: 2020-05-01 Source: ResearchSquare

    Background: Coronavirus disease MESHD (COVID-19) is rapidly spreading worldwide. Although 10%–20% of patients with COVID-19 have severe symptoms, little is known about the risk factors related to the aggravation of COVID-19 symptoms from asymptomatic TRANS or mild to severe disease MESHD states. Methods: This retrospective study included 211 patients who were asymptomatic TRANS or with mild presentations of COVID-19. We evaluated the differences in in demographic and clinical data between the cured (discharged to home) and transferred (aggravated to severe-stage COVID-19) groups. Results: A multivariate logistic analysis showed that body temperature, chills MESHD chills HP, initial chest X-ray findings, and the presence of diabetes were significantly associated with predicting the progression to severe stage of COVID-19 (p < 0.05). The odds ratio of transfer in patients with COVID-19 increased by 12.7-fold for abnormal findings such as haziness or consolidation in initial chest X-ray, 6.32-fold for initial symptom of chills MESHD chills HP, and 64.1-fold for diabetes.Conclusions: Even if patients are asymptomatic TRANS or have mild symptoms, clinicians should closely observe patients with COVID-19 presenting with chills MESHD chills HP, body temperature >37.5°C, findings of pneumonia MESHD pneumonia HP in chest X-ray, or diabetes.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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