Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
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    Risk factors for SARS-CoV-2 infection MESHD, hospitalisation, and death in Catalonia MESHD, Spain: a population-based cross-sectional study

    Authors: Judit Villar-Garcia; Rosa Maria Vivanco-Hidalgo; Montserrat Cleries; Elisenda Martinez; David Monterde; Pol Perez-Sust; Luis Garcia-Eroles; Carol Sais; Montserrat Moharra; Emili Vela; Jochen Lennerz; Hetal Desai Marble; Lauren L. Ritterhouse; Julie Batten; N. Zeke Georgantas; Rebecca Pellerin; Sylvia Signorelli; Julia Thierauf; Molly Kemball; Christian Happi; Donald S. Grant; Daouda Ndiaye; Katherine J. Siddle; Samar B Mehta; Jason B. Harris; Edward T Ryan; Virginia M. Pierce; Regina C LaRocque; Jacob Lemieux; Pardis Sabeti; Eric Rosenberg; John Branda; Sarah E Turbett; Gail Carson; Malcolm G Semple; Janet T Scott

    doi:10.1101/2020.08.26.20182303 Date: 2020-09-01 Source: medRxiv

    OBJECTIVE To identify the different subpopulations that are susceptible for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection MESHD and hospitalisation or death MESHD due to coronavirus disease MESHD 2019 (COVID-19) in Catalonia, Spain. DESIGN Cross-sectional study. SETTING Data collected from the Catalan Health Surveillance System (CatSalut) in Catalonia, a region of Spain. PARTICIPANTS Using data collected between 1 March and 1 June 2020, we conducted the following comparative analyses: people infected by SARS-CoV-2 (328 892) vs Catalonia's entire population (7 699 568); COVID-19 cases who required hospitalisation (37 638) vs cases who did not require hospitalisation (291 254); and COVID-19 cases who died during the study period vs cases who did not die during the study period (12 287). MAIN OUTCOME MEASURES Three clinical outcomes related to COVID-19 ( infection MESHD, hospitalisation, or death MESHD). We analysed sociodemographic and environment variables (such as residing in a nursing home) and the presence of previous comorbidities. RESULTS A total of 328 892 cases were considered to be infected with SARS-CoV-2 (4.27% of total population). The main risk factors for the diagnostic were: female TRANS gender TRANS (risk ratio [RR] =1.49; 95% confidence interval [95% CI] =1.48-1.50), age TRANS (45-64 years old; RR=1.02; 95% CI=1.01-1.03), high comorbidity burden (GMA index) (RR=3.03; 95% CI=2.97-3.09), reside in a nursing home (RR=11.82; 95% CI=11.66-11.99), and smoking (RR=1.06; 95% CI=1.05-1.07). During the study period, there were 37 638 (11.4 %) hospitalisations due to COVID-19, and the risk factors were: male TRANS gender TRANS (RR=1.45; 95% CI=1.43-1.48), age TRANS > 65 (RR=2.38; 95% CI=2.28-2.48), very low individual income (RR=1.03; 95% CI=0.97-1.08), and high burden of comorbidities (GMA index) (RR=5.15; 95% CI=4.89-5.42). The individual comorbidities with higher burden were obesity HP obesity MESHD (RR=1.23; 95% CI=1.20-1.25), chronic obstructive pulmonary disease HP chronic obstructive pulmonary disease MESHD (RR=1.19; 95% CI=1.15-1.22), heart failure MESHD (RR=1.19; 95% CI=1.16-1.22), diabetes mellitus HP diabetes mellitus MESHD (RR=1.07; 95% CI=1.04-1.10), and neuro-psychiatric MESHD comorbidities (RR=1.06; 95% CI=1.03-1.10). A total of 12 287 deaths (3.73%) were attributed to COVID-19, and the main risk factors were: male TRANS gender TRANS (RR=1.73; 95% CI=1.67-1.81), age TRANS > 65 (RR=37.45; 95% CI=29.23-47.93), residing in a nursing home (RR=9.22; 95% CI=8.81-9.65), and high burden of comorbidities (GMA index) (RR=5.25; 95% CI=4.60-6.00). The individual comorbidities with higher burden were: heart failure MESHD (RR=1.21; 95% CI=1.16-1.22), chronic kidney disease HP chronic kidney disease MESHD (RR=1.17; 95% CI=1.13-1.22), and diabetes mellitus HP diabetes mellitus MESHD (RR=1.10; 95% CI=1.06-1.14). These results did not change significantly when we considered only PCR-positive patients. CONCLUSIONS Female TRANS gender TRANS, age TRANS between 45 to 64 years old, high burden of comorbidities, and factors related to environment (nursing home) play a relevant role in SARS-CoV-2 infection MESHD and transmission TRANS. In addition, we found risk factors for hospitalisation and death MESHD due to COVID-19 that had not been described to date, including comorbidity burden, neuro-psychiatric disorders MESHD, and very low individual income. This study supports interventions for transmission TRANS control beyond stratify-and-shield strategies focused only on protecting those at risk of death. Future COVID-19 studies should examine the role of gender TRANS, the burden of comorbidities, and socioeconomic status in disease transmission TRANS, and should determine its relationship to workplaces, especially healthcare centres and nursing homes.

    Risk factors for severe outcomes of COVID-19: a rapid review

    Authors: Aireen Wingert; Jennifer Pillay; Michelle Gates; Samantha Guitard; Sholeh Rahman; Andrew Beck; Ben Vandermeer; Lisa Hartling; Corrado Pipan; Antonio Paolo Beltrami; Francesco Curcio; Wei Wu; Lishen Zhang; Xinyi Xia; Shukui Wang; Qianghu Wang; Sérgio Souza Costa; Vitória Abreu de Carvalho; Vanda Maria Ferreira Simóes; Maria Teresa Seabra Soares de Britto e Alves; Alcione Miranda dos Santos; Alberto Pasqualetto; Maylin Koo; Virginia Esteve; Arnau Antoli; Rafael Moreno; Sergi Yun; Pau Cerda; Mariona Llaberia; Francesc Formiga; Marta Fanlo; Abelardo Montero; David Chivite; Olga Capdevila; Ferran Bolao; Xavier Pinto; Josep Llop; Antoni Sabate; Jordi Guardiola; Josep M Cruzado; Josep Comin-Colet; Salud Santos; Ramon Jodar; Xavier Corbella

    doi:10.1101/2020.08.27.20183434 Date: 2020-09-01 Source: medRxiv

    Background: Identification of high-risk groups is needed to inform COVID-19 vaccine prioritization strategies in Canada. A rapid review was conducted to determine the magnitude of association between potential risk factors and risk of severe outcomes of COVID-19. Methods: Methods, inclusion criteria, and outcomes were prespecified in a protocol that is publicly available. Ovid MEDLINE(R) ALL MESHD, Epistemonikos COVID-19 in LOVE Platform, and McMaster COVID-19 Evidence Alerts, and select websites were searched to 15 June 2020. Studies needed to be conducted in Organisation for Economic Co-operation and Development countries and have used multivariate analyses to adjust for potential confounders. After piloting, screening, data extraction, and quality appraisal were all performed by a single reviewer. Authors collaborated to synthesize the findings narratively and appraise the certainty of the evidence for each risk factor-outcome association. Results: Of 3,740 unique records identified, 34 were included in the review. The studies included median 596 (range 44 to 418,794) participants with a mean age TRANS between 42 and 84 years. Half of the studies (17/34) were conducted in the United States and 19/34 (56%) were rated as good quality. There was low or moderate certainty evidence for a large ([≥]2-fold) association with increased risk of hospitalization in people having confirmed COVID-19, for the following risk factors: obesity class III HP obesity class III MESHD, heart failure MESHD, diabetes MESHD, chronic kidney disease HP chronic kidney disease MESHD, dementia HP dementia MESHD, age TRANS over 45 years (vs. younger), male TRANS gender TRANS, Black race/ethnicity (vs. non-Hispanic white), homelessness, and low income (vs. above average). Age TRANS over 60 and 70 years may be associated with large increases in the rate of mechanical ventilation and severe disease, respectively. For mortality, a large association with increased risk may exist for liver disease MESHD, Bangladeshi ethnicity (vs. British white), age TRANS over 45 years (vs. <45 years), age TRANS over 80 years (vs. 65-69 years), and male TRANS gender TRANS in those 20-64 years (but not older). Associations with hospitalization and mortality may be very large ([≥]5-fold increased risk) for those aged TRANS over 60 years. Conclusion: Among other factors, increasing age TRANS (especially >60 years) appears to be the most important risk factor for severe outcomes among those with COVID-19. There is a need for high quality primary research (accounting for multiple confounders) to better understand the level of risk that might be associated with immigration or refugee status, religion or belief system, social capital, substance use disorders, pregnancy, Indigenous identity, living with a disability, and differing levels of risk among children TRANS. PROSPERO registration: CRD42020198001

    Clinical Characteristics, Comorbidities, Initial Management and Outcome of COVID-19 Infected Patients Admitted to Intensive Care Unit in Somalia: A National Retrospective Study.

    Authors: Mohamed Farah Yusuf Mohamud; Abdullahi Said Hashi; Abdikarim Hussein Mohamed; Ali Mohamed Yusuf; Ibrahim Hussein Ali; Mohamed Abdi Ahmed

    doi:10.21203/rs.3.rs-66767/v1 Date: 2020-08-27 Source: ResearchSquare

    Purpose: To investigate the clinical characteristics, morbidities, management, and outcomes of COVID-19 Infected patients admitted to the intensive care unit (ICU) in Somalia.Material MESHD and methods: We conducted a retrospective observational study of laboratory 60 confirmed patients with severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) admitted to an ICU from March 28, to May 28, 2020.The sociodemographic characteristics, comorbidities, exposure history, clinical manifestations (symptoms and signs), laboratory findings, treatment, and outcomes were collected from medical records.Results: Most of the patients admitted to ICU were men over 59 years of age TRANS, and nearly half had diabetes MESHD followed by hypertension HP hypertension MESHD chronic kidney disease HP and asthma HP asthma MESHD. The most clinical presentations were dyspnea HP dyspnea MESHD (91.2%), Fever HP Fever MESHD (81.1%), (68.75%), Fatigue HP and myalgia HP myalgia MESHD (25%), and Altered level of conscious (16.6%). Among 48 patients admitted to the ICU, about 24 (50%) patients had required endotracheal intubation and mechanical ventilation, and 11(29.9%) patients needed noninvasive ventilation, while 13(27.08%) patients treated with high-flow oxygen therapy >15 L/min (Table 3). Corticosteroids were administered to most patients (85.4%), while 77.1% of the patients received inhaled bronchodilators and morethan half of the patients administered antibiotics. 58.3% of the patients had received Oseltamivir, while 22.9% received Vasopressors.Conclusion This study represents the first description of critically ill MESHD patients infected with SARS-CoV-2 admitted to ICU in Somalia. The study identified that elder age TRANS, male TRANS gender TRANS, and diabetic MESHD and hypertensive MESHD comorbidities as independent risk factors of poor outcomes for patients admitted to the ICU (p<0.005).

    Trends in Covid-19 risk-adjusted mortality rates in a single health system

    Authors: Leora Horwitz; Simon A. Jones; Robert J. Cerfolio; Fritz Francois; Joseph Greco; Bret Rudy; Christopher M Petrilli; Ishan Paranjpe; Jessica K De Freitas; Tingyi Wanyan; Kipp W Johnson; Mesude Bicak; Eyal Klang; Young Joon Kwon; Anthony Costa; Shan Zhao; Riccardo Miotto; Alexander W Charney; Erwin Böttinger; Zahi A Fayad; Girish N Nadkarni; Fei Wang; Benjamin S Glicksberg; Laura J. Scott; Karen L. Mohlke; Kerrin S. Small

    doi:10.1101/2020.08.11.20172775 Date: 2020-08-14 Source: medRxiv

    Early reports showed high mortality from Covid-19; by contrast, the current outbreaks in the southern and western United States are associated with fewer deaths, raising hope that treatments have improved. However, in Texas for instance, 63% of diagnosed cases are currently under 50, compared to only 52% nationally in March-April. Current demographics in Arizona and Florida are similar. Therefore, whether decreasing Covid-19 mortality rates are a reflection of changing demographics or represent improvements in clinical care is unknown. We assessed outcomes over time in a single health system, accounting for changes in demographics and clinical factors. Methods We analyzed biweekly mortality rates for admissions between March 1 and June 20, 2020 in a single health system in New York City. Outcomes were obtained as of July 14, 2020. We included all hospitalizations with laboratory-confirmed Covid-19 disease. Patients with multiple hospitalizations (N=157, 3.3%) were included repeatedly if they continued to have laboratory-confirmed disease. Mortality was defined as in-hospital death MESHD or discharge to hospice care. Based on prior literature, we constructed a multivariable logistic regression model to generate expected risk of death MESHD, adjusting for age TRANS; sex; self-reported race and ethnicity; body mass index; smoking history; presence of hypertension HP hypertension MESHD, heart failure MESHD, hyperlipidemia HP hyperlipidemia MESHD, coronary artery disease MESHD, diabetes MESHD, cancer MESHD, chronic kidney disease HP chronic kidney disease MESHD, or pulmonary disease MESHD individually as dummy variables; and admission oxygen saturation, D-dimer, C reactive protein, ferritin, and cycle threshold for RNA detection. All data were obtained from the electronic health record. We then calculated the sum of observed and expected deaths in each two-week period and multiplied each period's observed/expected (O/E) risk by the overall average crude mortality to generate biweekly adjusted rates. We calculated Poisson control limits and indicated points outside the control limits as significantly different, following statistical process control standards. The NYU institutional review board approved the study and granted a waiver of consent. Results We included 4,689 hospitalizations, of which 4,661 (99.4%) had died or been discharged. The median age TRANS, and the proportion male TRANS or with any comorbidity decreased over time; median real-time PCR cycle threshold increased (indicating relatively less concentration of virus) (Table). For instance, median age TRANS decreased from 67 years in the first two weeks to 49 in the last two. Peak hospitalizations were during the fifth and sixth study weeks, which accounted for 40% of the hospitalizations. Median length of stay for patients who died or were discharged to hospice was 8 days (interquartile range, 4-16). Unadjusted mortality dropped each period, from 30.2% in the first two weeks to 3% in the last two weeks, with the last eight weeks being lower than the 95% control limits. Risk adjustment partially attenuated the mortality decline, but adjusted mortality rates in the second-to-last two weeks remained outside the control limits (Figure, Table). The O/E risk of mortality decreased from 1.07 (0.64-1.67) in the first two weeks to 0.39 (0.08-1.12) in the last two weeks. Discussion In this 16-week study of Covid-19 mortality at a single health system, we found that changes in demographics and severity of illness at presentation account for some, but not all, of the decrease in unadjusted mortality. Even after risk adjustment for a variety of clinical and demographic factors, mortality was significantly lower towards the end of the study period. Incremental improvements in outcomes are likely a combination of increasing clinical experience, decreasing hospital volume, growing use of new pharmacologic treatments (such as corticosteroids, remdesivir and anti-cytokine treatments), non-pharmacologic treatments (such as proning), earlier intervention, community awareness, and lower viral load exposure from increasing mask wearing and social distancing. It is also possible that earlier periods had a more virulent circulating strain. In summary, data from one health system suggest that Covid-19 remains a serious disease for high risk patients, but that outcomes may be improving.

    Diabetic MESHD Patients with Comorbidities had Worse Outcomes When Suffered with COVID-19 and Acarbose might have Protective Effects

    Authors: Weihua Hu, MD; Shunkui Luo; Zhanjin Lu, MD; Chang Li; Qijian Chen; Yameng Fan; Zaishu Chen; Longlong Wu; Jianfang Ye; Shiyan Chen; Junlu Tong; Lingling Wang; Jin Mei; Hongyun Lu

    doi:10.21203/rs.3.rs-57456/v1 Date: 2020-08-11 Source: ResearchSquare

    Background: Previous studies showed that diabetes MESHD was a common comorbidity of COVID-19, but the effects of diabetes MESHD or anti- diabetic MESHD drugs on the mortality of COVID-19 have not been well described. To investigate the outcome of different status (with or without comorbidity) and anti- diabetic MESHD medication before admission of diabetic MESHD patients after SARS-CoV-2 infected MESHD, we collected clinical data of COVID-19 patients from Hubei Province and compared between diabetes MESHD and non-diabetes MESHD.Methods: In this multicenter and retrospective study, we enrolled 1,422 cases of consecutive hospitalized patients from January 21, 2020 to March 25, 2020 at six hospitals in Hubei Province, China. The primary endpoint was in-hospital mortality.Results: Diabetes MESHD patients were 10-years older than non-diabetes MESHD (p<0.001), had higher prevalence SERO of comorbidities such as hypertension HP hypertension MESHD (p<0.001), coronary heart disease MESHD (p<0.001), cerebrovascular disease MESHD ( CVD MESHD) (p<0.001), chronic kidney disease HP chronic kidney disease MESHD ( CKD MESHD) (p=0.007). The incidence of mortality (p=0.003) were more prevalent among the diabetes MESHD group. Further analysis revealed that diabetes MESHD patients who took alpha-glucosidase inhibitor ( AGI MESHD) had lower mortality rate(p<0.01). Multivariable Cox regression showed that male TRANS sex, hypertension HP hypertension MESHD, CKD MESHD, CVD MESHD, age TRANS were risk factors for the mortality of COVID-19. Survival curve revealed that, compared with diabetes MESHD only group, the mortality was increased in diabetes MESHD with comorbidities (p=0.009), but had no significant difference in the non-comorbidity group, p=0.59).Conclusions: Patients with diabetes MESHD had worse outcome when suffered with COVID-19, however, it was not associated with diabetes MESHD itself but the comorbidities. Furthermore, the administration of AGI could reduce the risk of death MESHD in patients with diabetes MESHD.

    Association of Diabetes MESHD and Outcomes in Patients with COVID-19: A Propensity Score Matched Analyses from a French Retrospective Cohort

    Authors: Willy Sutter; Baptiste Duceau; Aurélie Carlier; Antonin Trimaille; Thibaut Pommier; Oriane Weizman; Joffrey Cellier; Laura Geneste; Vassili Panagides; Wassima Marsou; Antoine Deney; Sabir Attou; Thomas Delmotte; Sophie Ribeyrolles; Pascale Chemaly; Clément Karsenty; Gauthier Giordano; Alexandre Gautier; Corentin Chaumont; Pierre Guilleminot; Audrey Sagnard; Julie Pastier; maxime Vignac; delphine Mika; Charles Fauvel; Théo Pezel; Ariel Cohen; Guillaume Bonnet; Ronan Roussel; Louis POTIER

    doi:10.21203/rs.3.rs-51775/v1 Date: 2020-07-31 Source: ResearchSquare

    Background: To compare the clinical outcomes between patients with and without diabetes MESHD admitted to hospital with COVID-19.Methods: Retrospective multicentre cohort study from 24 academic tertiary medical centres in France including 2851 patients (675 with diabetes MESHD) hospitalised for COVID-19 between February 26 and April 20, 2020. A propensity score matching method (1:1 matching including patient characteristics, medical history, vital signs, and laboratory results) was used to compare patients with and without diabetes MESHD (n=603 in each group). The primary outcome was admission to intensive care unit (ICU) or in-hospital death. Results: Patients with diabetes MESHD were older (71 ± 13 vs. 65 ± 18 years; p<0.001), were less often female TRANS (38% vs. 44%; p<0.001) and more likely to have comorbidities: hypertension HP hypertension MESHD (79% vs 42%; p<0.001), coronary heart disease MESHD (23% vs 9%; p<0.001), stroke HP stroke MESHD (13% vs 8%; p<0.001), heart failure MESHD (17% vs 9%; p<0.001), chronic kidney disease HP chronic kidney disease MESHD (26% vs 10%; p<0.001), and chronic obstructive pulmonary disease HP chronic obstructive pulmonary disease MESHD (7% vs 5%; p<0.05). The primary outcome occurred in 584 (36.4%) patients with diabetes MESHD compared to 246 (26.8%) in those without diabetes MESHD (p<0.001). After propensity score matching, the risk of primary outcome was similar in patients with and without diabetes MESHD (hazard ratio [HR] 1.16, 95%CI 0.95-1.41, p=0.14) and was 1.29 (95%CI 0.97 – 1.69) for in-hospital mortality, 1.26 (95%CI 0.93 – 1.72) for mortality without transfer in ICU, and 1.14 (95%CI 0.88 – 1.47) for transfer to ICU.Conclusions: In this retrospective cohort of patients hospitalised for COVID-19, diabetes MESHD was not significantly associated with a higher risk of COVID-19 severe outcomes after propensity score matching.Trial registration NCT04344327

    Risk Factors for COVID-19-associated hospitalization: COVID-19-Associated Hospitalization Surveillance Network and Behavioral Risk Factor Surveillance System

    Authors: Jean Y. Ko; Melissa L. Danielson; Machell Town; Gordana Derado; Kurt J. Greenland; Pam Daily Kirley; Nisha B. Alden; Kimberly Yousey-Hindes; Evan J. Anderson; Patricia A. Ryan; Sue Kim; Ruth Lynfield; Salina M. Torres; Grant R. Barney; Nancy M. Bennett; Melissa Sutton; H. Keipp Talbot; Mary Hill; Aron J. Hall; Alicia M. Fry; Shikha Garg; Lindsay Kim; - COVID-NET Investigation Group

    doi:10.1101/2020.07.27.20161810 Date: 2020-07-29 Source: medRxiv

    Background: Identification of risk factors for COVID-19-associated hospitalization is needed to guide prevention and clinical care. Objective: To examine if age TRANS, sex, race/ethnicity, and underlying medical conditions is independently associated with COVID-19-associated hospitalizations. Design: Cross-sectional. Setting: 70 counties within 12 states participating in the Coronavirus Disease MESHD 2019-Associated Hospitalization Surveillance Network (COVID-NET) and a population-based sample of non-hospitalized adults TRANS residing in the COVID-NET catchment area from the Behavioral Risk Factor Surveillance System. Participants: U.S. community-dwelling adults TRANS ([≥]18 years) with laboratory-confirmed COVID-19-associated hospitalizations, March 1- June 23, 2020. Measurements: Adjusted rate ratios (aRR) of hospitalization by age TRANS, sex, race/ethnicity and underlying medical conditions ( hypertension HP hypertension MESHD, coronary artery disease MESHD, history of stroke HP stroke MESHD, diabetes MESHD, obesity HP obesity MESHD [BMI [≥]30 kg/m2], severe obesity HP obesity MESHD [BMI[≥]40 kg/m2], chronic kidney disease HP chronic kidney disease MESHD, asthma HP asthma MESHD, and chronic obstructive pulmonary disease HP chronic obstructive pulmonary disease MESHD). Results: Our sample included 5,416 adults TRANS with COVID-19-associated hospitalizations. Adults TRANS with (versus without) severe obesity HP obesity MESHD (aRR:4.4; 95%CI: 3.4, 5.7), chronic kidney disease HP chronic kidney disease MESHD (aRR:4.0; 95%CI: 3.0, 5.2), diabetes MESHD (aRR:3.2; 95%CI: 2.5, 4.1), obesity HP obesity MESHD (aRR:2.9; 95%CI: 2.3, 3.5), hypertension HP hypertension MESHD (aRR:2.8; 95%CI: 2.3, 3.4), and asthma HP asthma MESHD (aRR:1.4; 95%CI: 1.1, 1.7) had higher rates of hospitalization, after adjusting for age TRANS, sex, and race/ethnicity. In models adjusting for the presence of an individual underlying medical condition, higher hospitalization rates were observed for adults TRANS [≥]65 years, 45-64 years (versus 18-44 years), males TRANS (versus females TRANS), and non-Hispanic black and other race/ethnicities (versus non-Hispanic whites). Limitations: Interim analysis limited to hospitalizations with underlying medical condition data. Conclusion: Our findings elucidate groups with higher hospitalization risk that may benefit from targeted preventive and therapeutic interventions.

    Predicting Critical State after COVID-19 Diagnosis Using Real-World Data from 20152 Confirmed US Cases TRANS

    Authors: Mike Domenik Rinderknecht; Yannick Klopfenstein

    doi:10.1101/2020.07.24.20155192 Date: 2020-07-27 Source: medRxiv

    The global COVID-19 pandemic caused by the virus SARS-CoV-2 has led to over 10 million confirmed cases TRANS, half a million deaths, and is challenging healthcare systems worldwide. With limited medical resources, early identification of patients with a high risk of progression to severe disease MESHD or a critical state is crucial. We present a prognostic model predicting critical state within 28 days following COVID-19 diagnosis trained on data from US electronic health records (EHR) within IBM Explorys, including demographics, comorbidities, symptoms, laboratory test results, insurance types, and hospitalization. Our entire cohort included 20152 COVID-19 cases, of which 3160 patients went into critical state or died. Random, stratified train-test splits were repeated 100 times to obtain a distribution of performance SERO. The median and interquartile range of the areas under the receiver operating characteristic curve (ROC AUC) and the precision recall SERO curve (PR AUC) were 0.863 [0.857, 0.866] and 0.539 [0.526, 0.550], respectively. Optimizing the decision threshold lead to a sensitivity SERO of 0.796 [0.775, 0.821] and a specificity of 0.784 [0.769, 0.805]. Good model calibration was achieved, showing only minor tendency to over-forecast probabilities above 0.6. The validity of the model was demonstrated by the interpretability analysis confirming existing evidence on major risk factors (e.g., higher age TRANS and weight, male TRANS gender TRANS, diabetes MESHD, cardiovascular disease MESHD disease, and chronic kidney HP chronic kidney disease MESHD). The analysis also revealed higher risk for African Americans and "self-pay patients". To the best of our knowledge, this is the largest dataset based on EHR used to create a prognosis model for COVID-19. In contrast to large-scale statistics computing odds ratios for individual risk factors, the present model combining a rich set of covariates can provide accurate personalized predictions enabling early treatment to prevent patients from progressing to a severe or critical state.

    Modeling the progression of SARS-CoV-2 infection MESHD in patients with COVID-19 risk factors through predictive analysis

    Authors: Juan Alonso Leon-Abarca

    doi:10.1101/2020.07.14.20154021 Date: 2020-07-19 Source: medRxiv

    With almost a third of adults TRANS being obese MESHD, another third hypertense MESHD and almost a tenth affected by diabetes MESHD, Latin American countries could see an elevated number of severe COVID-19 outcomes. We used the Open Dataset of Mexican patients with COVID-19 suspicion who had a definite RT-PCR result to develop a statistical model that evaluated the progression of SARS-CoV-2 infection MESHD in the population. We included patients of all ages TRANS with every risk factor provided by the dataset: asthma HP, chronic obstructive pulmonary disease HP chronic obstructive pulmonary disease MESHD, smoking, diabetes MESHD, obesity HP obesity MESHD, hypertension HP hypertension MESHD, immunodeficiencies HP immunodeficiencies MESHD, chronic kidney disease HP chronic kidney disease MESHD, cardiovascular diseases MESHD, and pregnancy. The dataset also included an unspecified category for other risk factors that were not specified as a single variable. To avoid excluding potential patients at risk, that category was included in our analysis. Due to the nature of the dataset, the calculation of a standardized comorbidity index was not possible. Therefore, we treated risk factors as a categorical variable with two categories: absence of risk factors and the presence of at least one risk factor in accordance with previous epidemiological reports. Multiple logistic regressions were carried out to associate sex, risk factors, and age TRANS as a continuous variable (and the interaction that accounted for increasing diseases with older ages TRANS); and SARS-CoV-2 infection MESHD as the dependent zero-one binomial variable. Post estimation predictive marginal analysis was performed to generate probability trends along 95% confidence bands. This analysis was repeated several times through the course of the pandemic since the first record provided in their repository (April 12, 2020) to one month after the end of the state of sanitary emergency (the last date analyzed: June 27, 2020). After processing, the last measurement included 464,389 patients. The baseline analysis on April 12 revealed that people 35 years and older with at least one risk factor had a lower risk of SARS-CoV-2 infection MESHD in comparison to patients without risk factors (Figure 1). One month before the end of the nationwide state of emergency this age TRANS threshold was found at 50 years (May 2, 2020) and it shifted to 65 years on May 30. Two weeks after the end of the public emergency (June 13, 2020) the trends converged at 80 years and one week later (June 27, 2020) every male TRANS and female TRANS patient with at least one risk factor had a higher risk of SARS-CoV-2 infection MESHD compared to people without risk factors. Through the course of the COVID-19 pandemic, all four probability curves shifted upwards as a result of progressive disease spread TRANS. In conclusion, we found our model could monitor accurately the probability of SARS-CoV-2 infection MESHD in relation to age TRANS, sex, and the presence of at least one risk factor. Also, because the model can be applied to any particular political region within Mexico, it could help evaluate the contagion spread in specific vulnerable populations. Further studies are needed to determine the underlying nature of the mechanisms behind such observations.

    Hospital mortality and resource implications of hospitalisation with COVID-19 in London, UK: a prospective cohort study

    Authors: Savvas Vlachos; Adrian Wong; Victoria Metaxa; Sergio Canestrini; Carmen Lopez Soto; Jimstan Periselneris; Kai Lee; Tanya Patrick; Christopher Stovin; Katrina Abernethy; Budoor Albudoor; Rishi Banerjee; Fatimah Juma; Sara Al-Hashimi; William Bernal; Ritesh Maharaj

    doi:10.1101/2020.07.16.20155069 Date: 2020-07-17 Source: medRxiv

    Background Coronavirus disease MESHD 2019 (COVID-19) had a significant impact on the National Health Service in the United Kingdom (UK), with over 33 000 cases reported in London by July 6, 2020. Detailed hospital-level information on patient characteristics, outcomes and capacity strain are currently scarce but would guide clinical decision-making and inform prioritisation and planning. Methods We aimed to determine factors associated with hospital mortality and describe hospital and ICU strain by conducting a prospective cohort study at a tertiary academic centre in London, UK. We included adult TRANS patients admitted to hospital with laboratory-confirmed COVID-19 and followed them up until hospital discharge or 30 days. Baseline factors that are associated with hospital mortality were identified via semi-parametric and parametric survival analyses. Results Our study included 429 patients; 18% of them were admitted to ICU, 52% met criteria for ICU outreach team activation and 61% had treatment limitations placed during their admission. Hospital mortality was 26% and ICU mortality was 34%. Hospital mortality was independently associated with increasing age TRANS, male TRANS sex, history of chronic kidney disease HP chronic kidney disease MESHD, increasing baseline C-reactive protein level and dyspnoea MESHD at presentation. COVID-19 resulted in substantial ICU and hospital strain, with up to 9 daily ICU admissions and 41 daily hospital admissions, to a peak census of 80 infected MESHD patients admitted in ICU and 250 in the hospital. Management of such a surge required extensive reorganisation of critical care services with expansion of ICU capacity from 69 to 129 beds, redeployment of staff from other hospital areas and coordinated hospital-level effort. Conclusions COVID-19 is associated with a high burden of mortality for patients treated on the ward and the ICU and required substantial reconfiguration of critical care services. This has significant implications for planning and resource utilization.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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