Corpus overview


Overview

MeSH Disease

Infections (135)

Disease (117)

Death (94)

Coronavirus Infections (77)

Fever (63)


Human Phenotype

Fever (63)

Cough (48)

Pneumonia (47)

Fatigue (18)

Hypertension (14)


Transmission

Seroprevalence
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    Underdetection of COVID-19 cases in France in the exit phase following lockdown

    Authors: Giulia Pullano; Laura Di Domenico; Chiara E Sabbatini; Eugenio Valdano; Clément Turbelin; Marion Debin; Caroline Guerrisi; Charly Kengne-Kuetche; Cécile Souty; Thomas Hanslik; Thierry Blanchon; Pierre-Yves Boëlle; Julie Figoni; Sophie Vaux; Christine Campèse; Sibylle Bernard-Stoecklin; Vittoria Colizza

    doi:10.1101/2020.08.10.20171744 Date: 2020-08-12 Source: medRxiv

    A novel testing policy was implemented in May in France to systematically screen potential COVID-19 infections MESHD and suppress local outbreaks while lifting lockdown restrictions. 20,736 virologically- confirmed cases TRANS were reported in mainland France from May 13, 2020 (week 20, end of lockdown) to June 28 (week 26). Accounting for missing data and the delay from symptom onset TRANS to confirmation test, this corresponds to 7,258 [95% CI 7,160-7,336] cases with symptom onset TRANS during this period, a likely underestimation of the real number. Using age TRANS-stratified transmission TRANS models parameterized to behavioral data and calibrated to regional hospital admissions, we estimated that 69,115 [58,072-77,449] COVID-19 symptomatic cases occurred, suggesting that 9 out of 10 cases with symptoms were not ascertained. Median detection rate increased from 7% [6-9]% to 31% [28-35]% over time, with regional estimates varying from 11% (Grand Est) to 78% (Normandy) by the end of June. Healthcare-seeking behavior in COVID-19 suspect cases remained low (31%) throughout the period. Model projections for the incidence of symptomatic cases (4.5 [3.9-5.0] per 100,000) were compatible with estimates integrating participatory and virological surveillance data, assuming all suspect cases consulted. Encouraging healthcare-seeking behavior and awareness in suspect cases is critical to improve detection. Substantially more aggressive and efficient testing with easier access is required to act as a pandemic-fighting tool. These elements should be considered in light of the currently observed resurgence of cases in France and other European countries.

    Epidemiological Characteristics of COVID-19 under Government-mandated Control Measures in Inner Mongolia, China

    Authors: Sha Du; Haiwen Lu; Yuenan Su; Shufeng Bi; Jing Wu; Wenrui Wang; Xinhui Yu; Min Yang; Huiqiu Zheng; Xuemei Wang

    doi:10.21203/rs.3.rs-57472/v1 Date: 2020-08-11 Source: ResearchSquare

    BackgroundThere were 75 local confirmed cases TRANS during the COVID-19 epidemic followed by an outbreak of Wuhan in Inner Mongolia. The aims of our study were to provide reference to control measures of COVID-19 and scientific information for supporting government decision-making for serious infectious disease MESHD, in remote regions with relatively insufficient medical resources like Inner Mongolia.MethodsThe data published by Internet were summarized in order to describe the epidemiological and clinical characteristics of patients with COVID-19. The basic reproductive number (R TRANS 0 ), incubation period TRANS, time from illness onset to confirmed and the duration of hospitalization were analyzed. The composition of imported and local secondary cases TRANS and the mild/common and severe/critical cases among different ages TRANS, genders TRANS and major clinical symptoms were compared.ResultsIn 2020, from January 23 to February 19 (less than 1 month), 75 local cases of COVID-19 were confirmed in Inner Mongolia. Among them, the median age TRANS was 45 years old (34.0, 57.0), and 61.1% were male TRANS and 33 were imported (44.0%). 29 (38.7%) were detected through close contact TRANS tracking, more than 80.0% were mild/common cases. The fatality rate was 1.3% and the basic reproductive number (R TRANS 0 ) was estimated to be 2.3. The median incubation period TRANS was 8.5 days (6.0~12.0) and the maximum incubation period TRANS reached 28 days. There was a statistically difference in the incubation period TRANS between imported and local secondary cases TRANS ( P <0.001). The duration of hospitalization of patients with incubation period TRANS <8.5 days was higher than that of patients with incubation period TRANS ≥8.5 days (30.0 vs. 24.0 days).ConclusionIn Inner Mongolia, an early and mandatory control strategy by government associated with the rapidly reduced incidence of COVID-19, by which the epidemic growth was controlled completely. And the fatality rate of COVID-19 was relatively low.

    Value of laboratory tests in COVID-19 hospitalized patients for clinical decision-makers: a predictive model, using data mining approach

    Authors: Atefeh Mousavi; Soheyla Rezaei; Jamshid Salamzadeh; Ali Mirzazadeh; Farzad Peiravian; Nazila Yousefi

    doi:10.21203/rs.3.rs-56252/v1 Date: 2020-08-09 Source: ResearchSquare

    Purpose: Because of the rapid increase in confirmed cases TRANS of COVID-19, in particular those with severe or critical status, overwhelming of health systems is a worldwide concern. Therefore, identifying high-risk COVID-19 patients, can help service providers for priority setting and hospital resource allocation. Methods: 4542 adult TRANS patients with confirmed COVID-19 admitted in 15 hospitals in Tehran, Iran, from Feb 20 to April 18, 2020 were included in this retrospective cohort study with final outcomes of survived and died patients. Demographic features including age TRANS and sex, and laboratory data measured at admission were extracted and compared between recovered and died patients. Data analysis was performed applying SPSS modeler software using a logistic regression method.Results: Of 4542 hospitalized adult TRANS patients, 822 patients (18.09%) died during hospitalization, and 3720 (81.90%) recovered and discharged. Based on logistic regression model, older age TRANS, 40-49 (RR= 1.80, CI: 1.13-2.87), 50-59 (RR=2.63, CI: 1.71-4.02), 60-69 (RR= 4.40, CI: 2.92-6.63), 70-79 (RR=7.49, CI: 5.01-11.19), Above 80 (RR=13.85, CI: 9.23-2.77), ALT ≥ 55 IU/ (RR=2.20, CI: 1.69-2.86), AST ≥ 100 IU/L (RR=5.93, CI: 4.75-7.39), ALP ≥ 200 IU/L (RR=2.46, CI: 1.80-3.37), sodium < 135 mEq/l (RR=1.69, CI: 1.35-2.11) or more than 145 mEq/l (RR=7.24, CI: 5.07-10.33), potassium > 5.50 mEq/l (RR=7.53, CI: 4.15-13.64), and calcium < 8.50 mEq/l (RR=3.39, CI: 2.81-4.09), CPK between 307-600 IU/L (RR=2.73, CI: 2.12-3.53) and above 600 IU/L (RR=4.41, CI: 3.40-5.71) in men, and 192-400 IU/L (RR=2.73, CI: 2.12-3.53), and above 400 (RR=4.41, CI: 3.40-5.71) in women, CRP > 3 mg/l (RR=3.22, CI: 1.99-5.20), and creatinine > 1.5 mg/l (RR=6.37, CI: 5.30-7.66) were significantly associated with COVID-19 mortality. Conclusion: Our findings suggested less than one in five hospitalized patients with COVID-19 die mostly due to electrolyte disbalance, liver, and renal dysfunctions. Better supportive care is needed to improve outcomes for patients with COVID-19.

    CRISPR-based and RT-qPCR surveillance of SARS-CoV-2 in asymptomatic TRANS individuals uncovers a shift in viral prevalence SERO among a university population

    Authors: Jennifer N Rauch; Eric Valois; Jose Carlos Ponce-Rojas; Zach Aralis; Ryan L Lach; Francesca Zappa; Morgane Audouard; Sabrina C Solley; Chinmay Vaidya; Michael Costello; Holly Smith; Ali Javanbakht; Betsy Malear; Laura Polito; Stewart Comer; Katherine Arn; Kenneth S Kosik; Diego Acosta-Alvear; Maxwell Z Wilson; Lynn Fitzgibbons; Carolina Arias

    doi:10.1101/2020.08.06.20169771 Date: 2020-08-07 Source: medRxiv

    Background: The progress of the COVID-19 pandemic profoundly impacts the health of communities around the world, with unique impacts on colleges and universities. Transmission TRANS of SARS-CoV-2 by asymptomatic TRANS people is thought to be the underlying cause of a large proportion of new infections MESHD. However, the local prevalence SERO of asymptomatic TRANS and pre-symptomatic carriers TRANS of SARS-CoV-2 is influenced by local public health restrictions and the community setting. Objectives: This study has three main objectives. First, we looked to establish the prevalence SERO of asymptomatic TRANS SARS-CoV-2 infection MESHD on a university campus in California. Second, we sought to assess the changes in viral prevalence SERO associated with the shifting community conditions related to non-pharmaceutical interventions (NPIs). Third, we aimed to compare the performance SERO of CRISPR- and PCR-based assays for large-scale virus surveillance sampling in COVID-19 asymptomatic TRANS persons. Methods: We enrolled 1,808 asymptomatic TRANS persons for self-collection of oropharyngeal (OP) samples to undergo SARS-CoV-2 testing. We compared viral prevalence SERO in samples obtained in two time periods: May 28th-June 11th; June 23rd-July 2nd. We detected viral genomes in these samples using two assays: CREST, a CRISPR-based method recently developed at UCSB, and the RT-qPCR test recommended by US Centers for Disease MESHD Control and Prevention (CDC). Results: Of the 1,808 participants, 1,805 were affiliates of the University of California, Santa Barbara, and 1,306 were students. None of the tests performed on the 732 samples collected between late May to early June were positive. In contrast, tests performed on the 1076 samples collected between late June to early July, revealed nine positive cases. This change in prevalence SERO met statistical significance, p = 0.013. One sample was positive by RT-qPCR at the threshold of detection, but negative by both CREST and CLIA-confirmation testing. With this single exception, there was perfect concordance in both positive and negative results obtained by RT-qPCR and CREST. The estimated prevalence SERO of the virus, calculated using the confirmed cases TRANS, was 0.74%. The average age TRANS of our sample population was 28.33 (18-75) years, and the average age TRANS of the positive cases was 21.7 years (19-30). Conclusions: Our study revealed that there were no COVID-19 cases in our study population in May/June. Using the same methods, we demonstrated a substantial shift in prevalence SERO approximately one month later, which coincided with changes in community restrictions and public interactions. This increase in prevalence SERO, in a young and asymptomatic TRANS population which would not have otherwise accessed COVID-19 testing, indicated the leading wave of a local outbreak, and coincided with rising case counts in the surrounding county and the state of California. Our results substantiate that large, population-level asymptomatic TRANS screening using self-collection may be a feasible and instructive aspect of the public health approach within large campus communities, and the almost perfect concordance between CRISPR- and PCR-based assays indicate expanded options for surveillance testing

    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.

    A SEIR-like model with a time-dependent contagion factor describes the dynamics of the Covid-19 pandemic

    Authors: Ronald Dickman

    doi:10.1101/2020.08.06.20169557 Date: 2020-08-07 Source: medRxiv

    I consider a simple, deterministic SEIR-like model without spatial or age TRANS structure, including a presymptomatic state and distinguishing between reported and nonreported infected individuals. Using a time-dependent contagion factor {beta}(t) (in the form a piecewise constant function) and literature values for other epidemiological parameters, I obtain good fits to observational data for the cumulative number of confirmed cases TRANS in over 160 regions (103 countries, 24 Brazilian states and 34 U.S. counties). The evolution of {beta} is useful for characterizing the state of the epidemic. The analysis provides insight into general trends associated with the pandemic, such as the tendency toward reduced contagion, and the fraction of the population exposed to the virus.

    Epidemiology of Reopening in the COVID-19 Pandemic in the United States, Europe and Asia

    Authors: Weiqi Zhang; Alina Oltean; Scott Nichols; Fuad Odeh; Fei Zhong

    doi:10.1101/2020.08.05.20168757 Date: 2020-08-06 Source: medRxiv

    Since the discovery of the novel coronavirus (SARS-CoV-2), COVID-19 has become a global healthcare and economic crisis. The United States (US) and Europe exhibited wide impacts from the virus with more than six million cases by the time of our analysis. To inhibit spread, stay-at-home orders and other non-pharmaceutical interventions (NPIs) were instituted. Beginning late April 2020, some US states, European, and Asian countries lifted restrictions and started the reopening phases. In this study, the changes of confirmed cases TRANS, hospitalizations, and deaths MESHD were analyzed after reopening for 11 countries and 40 US states using an interrupted time series analysis. Additionally, the distribution of these categories was further analyzed by age TRANS due to the known increased risk in elderly TRANS patients. Reopening had varied effects on COVID-19 cases depending on the region. Recent increases in cases did not fully translate into increased deaths MESHD. Eight countries had increased cases after reopening while only two countries showed the same trend in deaths MESHD. In the US, 30 states had observed increases in cases while only seven observed increased deaths MESHD. In addition, we found that states with later reopening dates were more likely to have significant decreases in cases, hospitalizations, and deaths MESHD. Furthermore, age TRANS distributions through time were analyzed in relation to COVID-19 in the US. Younger age groups TRANS typically had an increased share of cases after reopening.

    Clinical course and severity outcome indicators among COVID 19 hospitalized patients in relation to comorbidities distribution Mexican cohort

    Authors: Genny Carrillo; Nina Mendez Dominguez; Kassandra D Santos Zaldivar; Andrea Rochel Perez; Mario Azuela Morales; Osman Cuevas Koh; Alberto Alvarez Baeza

    doi:10.1101/2020.07.31.20165480 Date: 2020-08-04 Source: medRxiv

    Introduction: COVID-19 affected worldwide, causing to date, around 500,000 deaths MESHD. In Mexico, by April 29, the general case fatality was 6.52%, with 11.1% confirmed case TRANS mortality and hospital recovery rate around 72%. Once hospitalized, the odds for recovery and hospital death MESHD rates depend mainly on the patients' comorbidities and age TRANS. In Mexico, triage guidelines use algorithms and risk estimation tools for severity assessment and decision-making. The study's objective is to analyze the underlying conditions of patients hospitalized for COVID-19 in Mexico concerning four severity outcomes. Materials and Methods: Retrospective cohort based on registries of all laboratory-confirmed patients with the COVID-19 infection MESHD that required hospitalization in Mexico. Independent variables were comorbidities and clinical manifestations. Dependent variables were four possible severity outcomes: (a) pneumonia MESHD pneumonia HP, (b) mechanical ventilation (c) intensive care unit, and (d) death MESHD; all of them were coded as binary Results: We included 69,334 hospitalizations of laboratory-confirmed and hospitalized patients to June 30, 2020. Patients were 55.29 years, and 62.61% were male TRANS. Hospital mortality among patients aged TRANS<15 was 9.11%, 51.99% of those aged TRANS >65 died. Male TRANS gender TRANS and increasing age TRANS predicted every severity outcome. Diabetes and hypertension MESHD hypertension HP predicted every severity outcome significantly. Obesity MESHD Obesity HP did not predict mortality, but CKD, respiratory diseases MESHD, cardiopathies were significant predictors. Conclusion: Obesity MESHD Obesity HP increased the risk for pneumonia MESHD pneumonia HP, mechanical ventilation, and intensive care admittance, but it was not a predictor of in-hospital death MESHD. Patients with respiratory diseases MESHD were less prone to develop pneumonia MESHD pneumonia HP, to receive mechanical ventilation and intensive care unit assistance, but they were at higher risk of in-hospital death MESHD.

    Characteristics of COVID-19 fatality cases in East Kalimantan, Indonesia

    Authors: Swandari Paramita; Ronny Isnuwardana; Krispinus Duma; Rahmat Bakhtiar; Muhammad Khairul Nuryanto; Riries Choiru Pramulia Yudia; Evi Fitriany; Meiliati Aminyoto

    doi:10.1101/2020.08.01.20166470 Date: 2020-08-04 Source: medRxiv

    Introduction. Coronavirus Disease MESHD (COVID-19) is caused by SARS-CoV-2 infection MESHD. On March 2, 2020, Indonesia announced the first confirmed cases TRANS of COVID-19 infection MESHD. East Kalimantan will play an important role as the new capital of Indonesia. There is attention to the preparedness of East Kalimantan to respond to COVID-19. We report the characteristics of COVID-19 fatality cases in here. Methods. We retrospectively analyzed the fatality cases of COVID-19 patients from the East Kalimantan Health Office information system. All patients were confirmed COVID-19 by RT-PCR examination. Results. By July 31, 2020, 31 fatality cases of patients had been identified as having confirmed COVID-19 in East Kalimantan. The mean age TRANS of the patients was 55.1 + 9.2 years. Most of the patients were men (22 [71.0%]) with age TRANS more than 60 years old (14 [45.2%]). Balikpapan has the highest number of COVID-19 fatality cases from all regencies. Hypertension MESHD Hypertension HP was the most comorbidities in the fatality cases of COVID-19 patients in East Kalimantan. Discussion. Older age TRANS and comorbidities still contributed to the fatality cases of COVID-19 patients in East Kalimantan, Indonesia. Hypertension MESHD Hypertension HP, diabetes, cardiovascular disease MESHD, and cerebrovascular disease MESHD were underlying conditions for increasing the risk of COVID-19 getting into a serious condition. Conclusion. Active surveillance for people older than 60 years old and having underlying diseases MESHD is needed for reducing the case fatality rate of COVID-19 in East Kalimantan. Keywords. Comorbidity, fatality cases, COVID-19, Indonesia.

    COVID-19 pandemic in Djibouti: epidemiology and the response strategy followed to contain the virus during the first two months, 17 March to 16 May 2020

    Authors: Mohamed Elhakim; Saleh Banoita Tourab; Ahmed Zouiten

    doi:10.1101/2020.08.03.20167692 Date: 2020-08-04 Source: medRxiv

    Background: First cases of COVID-19 were reported from Wuhan, China, in December 2019, and it progressed rapidly. On 30 January, WHO declared the new disease MESHD as a PHEIC, then as a Pandemic on 11 March. By mid-March, the virus spread widely; Djibouti was not spared and was hit by the pandemic with the first case detected on 17 March. Djibouti worked with WHO and other partners to develop a preparedness and response plan, and implemented a series of intervention measures. MoH together with its civilian and military partners, closely followed WHO recommended strategy based on four pillars: testing, isolating, early case management, and contact tracing TRANS. From 17 March to 16 May, Djibouti performed the highest per capita tests in Africa and isolated, treated and traced the contacts TRANS of each positive case, which allowed for a rapid control of the epidemic. Methods: COVID-19 data included in this study was collected through MoH Djibouti during the period from 17 March to 16 May 2020. Results: A total of 1,401 confirmed cases TRANS of COVID-19 were included in the study with 4 related deaths MESHD (CFR: 0.3%) and an attack rate TRANS of 0.15%. Males TRANS represented (68.4%) of the cases, with the age group TRANS 31-45 years old (34.2%) as the most affected. Djibouti conducted 17,532 tests, and was considered as a champion for COVID-19 testing in Africa with 18.2 tests per 1000 habitant. All positive cases were isolated, treated and had their contacts traced TRANS, which led to early and proactive diagnosis of cases and in turn yielded up to 95-98% asymptomatic TRANS cases. Recoveries reached 69% of the infected cases with R0 TRANS (0.91). The virus was detected in 4 regions in the country, with the highest percentage in the capital (83%). Conclusion: Djibouti responded to COVID-19 pandemic following an efficient and effective strategy, using a strong collaboration between civilian and military health assets that increased the response capacities of the country. Partnership, coordination, solidarity, proactivity and commitment were the pillars to confront COVID-19 pandemic.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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