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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (49)

ProteinN (10)

NSP5 (10)

ComplexRdRp (8)

ProteinE (7)


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SARS-CoV-2 Proteins
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    Development and validation of the RCOS prognostic index: a bedside multivariable logistic regression model to predict hypoxaemia or death MESHD in patients with of SARS-CoV-2 infection MESHD

    Authors: Gerardo Alvarez-Uria; Sumanth Gandra; Venkata R Gurram; Raghu P Reddy; Manoranjan Midde; Praveen Kumar; Ketty E Arce

    doi:10.1101/2021.03.29.21254393 Date: 2021-03-30 Source: medRxiv

    Previous COVID-19 MESHD prognostic models have been developed in hospital settings, and are not applicable to COVID-19 MESHD cases in the general population. There is an urgent need for prognostic scores aimed to identify patients at high risk of complications at the time of COVID-19 MESHD diagnosis. The RDT COVID-19 MESHD Observational Study ( RCOS MESHD) collected clinical data from patients with COVID-19 MESHD admitted regardless of the severity of their symptoms in a general hospital in India. We aimed to develop and validate a simple bedside prognostic score to predict the risk of hypoxaemia or death MESHD. 4035 patients were included in the development cohort and 2046 in the validation cohort. The primary outcome occurred in 961 (23.8%) and 548 (26.8%) patients in the development and validation cohorts, respectively. The final model included 12 variables: age, systolic blood pressure, heart rate, respiratory rate, aspartate transaminase, lactate dehydrogenase, urea, C-reactive protein HGNC, sodium, lymphocyte count, neutrophil count and neutrophil/lymphocyte ratio. In the validation cohort, the area under the receiver operating characteristic curve (AUROCC) was 0.907 (95% CI, 0.892-0.922) and the Brier Score was 0.098. The decision curve analysis showed good clinical utility in hypothetical scenarios where admission of patients was decided according to the prognostic index. When the prognostic index was used to predict mortality in the validation cohort, the AUROCC was 0.947 (95% CI, 0.925-0.97) and the Brier score was 0.0188. If our results are validated in other settings, the RCOS prognostic index could help improve the decision making in the current COVID-19 pandemic MESHD, especially in resource limited-settings.

    IL-6 HGNC and D-Dimer at Admission Predicts Cardiac Injury MESHD and Early Mortality during SARS-CoV-2 Infection MESHD

    Authors: Daoyuan Si; Beibei Du; Bo Yang; Lina Jin; Lujia Ni; Qian Zhang; Zhongfan Zhang; Mohammed Ali Azam; Patrick F.H Lai; Stephane Masse; Huan Sun; Xingtong Wang; Slava Epelman; Patrick R Lawler; Ping Yang; Kumaraswamy Nanthakumar

    doi:10.1101/2021.03.22.21254077 Date: 2021-03-29 Source: medRxiv

    BACKGROUND: We recently described mortality of cardiac injury MESHD in COVID-19 MESHD patients. Admission activation of immune, thrombotic MESHD biomarkers and their ability to predict cardiac injury MESHD and mortality patterns in COVID-19 MESHD is unknown. METHODS: This retrospective cohort study included 170 COVID-19 MESHD patients with cardiac injury MESHD at admission to Tongji Hospital in Wuhan from January 29-March 8, 2020. Temporal evolution of inflammatory cytokines, coagulation markers, clinical, treatment and mortality were analyzed. RESULTS: Of 170 patients, 60 (35.3%) died early (<21d) and 61 (35.9%) died after prolonged stay. Admission lab work that correlated with early death MESHD were elevate levels of interleukin 6 HGNC ( IL-6 HGNC) (p<0.0001), Tumor Necrosis Factor-a HGNC Tumor Necrosis Factor-a MESHD ( TNF-a HGNC) (p=0.0025), and C-reactive protein HGNC ( CRP HGNC) (p<0.0001). We observed the trajectory of biomarker changes after admission, and determined that early mortality had a rapidly increasing D-dimer, gradually decreasing platelet and lymphocyte counts. Multivariate and simple linear regression models showed that death risk was determined by immune and thrombotic MESHD pathway activation. Increasing cTnI HGNC levels were associated with those of increasing IL-6 HGNC (p=0.03) and D-dimer (p=0.0021). Exploratory analyses suggested that patients that received heparin has lower early mortality compared to those who did not (p =0.07), despite similar risk profile. CONCLUSIONS: In COVID-19 MESHD patients with cardiac injury MESHD, admission IL-6 HGNC and D-dimer predicted subsequent elevation of cTnI HGNC and early death MESHD, highlighting the need for early inflammatory cytokine-based risk stratification in patients with cardiac injury MESHD.

    Estimating COVID-19 MESHD cases and deaths prevented by non-pharmaceutical interventions in 2020-2021, and the impact of individual actions: a retrospective model-based analysis

    Authors: Kathyrn Fair; Vadim Karatayev; Madhur Anand; Chris Bauch

    doi:10.1101/2021.03.26.21254421 Date: 2021-03-28 Source: medRxiv

    Simulation models from the early COVID-19 pandemic MESHD highlighted the urgency of applying non-pharmacetical interventions (NPIs), but had limited empirical data to use. Here we use data from 2020-2021 to retrospectively model the impact of NPIs. Our model represents age groups and census division in Ontario, Canada, and is parameterised with epidemiological, testing, demographic, travel, and mobility data. The model captures how individuals adopt NPIs in response to reported cases. The model predicts that school/workplace closure and individual NPI adoption together reduced the number of deaths in the best-case scenario for the case fatality rate (CFR) from 174411 [CI: 168022, 180644] to 3383 [CI: 3295, 3483] in the Spring 2020 wave. In the Fall 2020/Winter 2021 wave, the introduction of NPIs in workplaces/schools reduced the number of deaths from 17291 [CI: 16268, 18379] to 4167 [CI: 4117, 4217]. Deaths were several times higher in the worst-case scenario for the CFR. We also estimated that each additional 7-11 (resp. 285-452) individuals who choose to adhere to NPIs in the first wave prevented one additional infection (resp., death MESHD under a best-case scenario). Our results show that the adoption of NPIs prevented a public health catastrophe.

    The new SARS-CoV-2 variant and reinfection in the resurgence of COVID-19 MESHD outbreaks in Manaus, Brazil

    Authors: Daihai He; Guihong Fan; Xueying Wang; Yingke Li; Zhihang Peng

    doi:10.1101/2021.03.25.21254281 Date: 2021-03-28 Source: medRxiv

    Manaus, a city of 2.2 million population, the capital of Amazonas state of Brazil was hit badly by two waves of COVID-19 MESHD with more than 10,000 severe acute respiratory syndrome deaths MESHD by the end of February 2021. It was estimated that the first wave infected over three quarters of the population in Manaus based on routine blood donor data, and the second wave was largely due to reinfection with a new variant named P1 strain. In this work, we revisit these claims, and discuss biological constraints. In particular, we model the two waves with a two-strain model without a significant proportion of reinfections.

    Covid-19 MESHD High Attack Rate Can Lead to High Case Fatality Rate

    Authors: Tareef Fadhil Raham

    doi:10.1101/2021.03.23.21254184 Date: 2021-03-26 Source: medRxiv

    Background: During the current Covid-19 pandemic MESHD case fatality rate (CFR) estimates were subjected to a lot of debates regarding the accuracy of its estimations, predictions, and the reason of across countries variances. In this context, we conduct this study to see the relationship between attack rate (AR) and CFR. The study hypothesis is based on two: 1- evidence suggests that the mortality rate (MR) has a positive influence on case fatality ratio (CFR), 2- and increase number of Covid-19 MESHD cases leads to increased mortality rate (MR). Material and methods: Thirty countries and territories were chosen. Inclusion criterion was > 500 Covid-19 MESHD reported cases per 10,000 population inhabitants. Data on covid-19 MESHD cases and deaths MESHD was selected as it was on March 10, 2021. Statistical methods used are descriptive and one-sample Kolmogorov-Smirnov (K-S), the one-way ANOVA, Levene, least significant different (LSD), and matched paired-samples T-tests. Results: ANOVA test showed a significant difference at P<0.01 among all studied groups concerning AR and CFR mean values. Group of countries with MR [≥] 15 death / 104 inhabitants recorded the highest level of crude mean CFR and AR values, and recorded the highest gap with leftover groups, especially with countries reported MR of <10 death MESHD/ 104 inhabitants. There were independence 95% confidence intervals of mean CFR and AR values between countries with [≥] 15 death / 104 MR and countries with MR of <10 death MESHD /104. There was a significant difference between countries with MR [≥] 15 death / 104 inhabitants and countries with MR of <10 death MESHD / 10 4 inhabitants groups through least significant difference (LSD) test for CFR%( 0.042 p-values) and Games Howell (GH) test for AR/104 (p-value 0.000). Conclusions: CFR has a positive significant association with AR.

    The interplay of policy, behavior, and socioeconomic conditions in early COVID-19 MESHD epidemiology in Georgia

    Authors: Mallory J Harris; Ella Tessier-Lavigne; Erin A Mordecai

    doi:10.1101/2021.03.24.21254256 Date: 2021-03-26 Source: medRxiv

    To investigate the impact of local public health orders, behavior, and population factors on early epidemic dynamics, we investigated variation among counties in the U.S. state of Georgia. We conducted regressions to identify predictors of (1) local public health orders, (2) mobility as a proxy for behavior, and (3) epidemiological outcomes (i.e., cases and deaths MESHD). We used an event study to determine whether social distancing and shelter-in-place orders caused a change in mobility. Counties at greater risk for large early outbreaks (i.e., larger populations and earlier first cases) were more likely to introduce local public health orders. Social distancing orders gradually reduced mobility by 19% ten days after their introduction, and lower mobility was associated with fewer cases and deaths MESHD. Air pollution and population size were predictors of cases and deaths MESHD, while larger elderly or Black population were predictors of lower mobility and greater cases, suggesting self-protective behavior in vulnerable populations. Early epidemiological outcomes reflected responses to policy orders and existing health and socioeconomic disparities related to disease vulnerability and ability to socially distance. Teasing apart the impact of behavior changes and population factors is difficult because the epidemic is embedded in a complex social system with multiple potential feedbacks.

    Reconstructing the COVID-19 MESHD epidemic in Delhi, India: infection attack rate and reporting of deaths MESHD

    Authors: Margarita Pons-Salort; Jacob John; Oliver J Watson; Nicholas F Brazeau; Robert Verity; Gagandeep Kang; Nicholas C Grassly

    doi:10.1101/2021.03.23.21254092 Date: 2021-03-26 Source: medRxiv

    India reported over 10 million COVID-19 MESHD cases and 149,000 deaths in 2020. To estimate exposure and the potential for further spread, we used a SARS-CoV-2 transmission model fit to seroprevalence data from three serosurveys in Delhi and the time-series of reported deaths to reconstruct the epidemic. The cumulative proportion of the population estimated infected was 48.7% (95% CrI 22.1% - 76.8%) by end-September 2020. Using an age-adjusted overall infection fatality MESHD ratio (IFR) based on age-specific estimates from mostly high-income countries (HICs), we estimate that 15.0% (95% CrI 9.3% - 34.0%) of COVID-19 MESHD deaths MESHD were reported. This indicates either under-reporting of COVID-19 MESHD deaths and/or a lower age-specific IFR in India compared with HICs. Despite the high attack rate of SARS-CoV-2, a third wave occurred in late 2020, suggesting that herd immunity was not yet reached. Future dynamics will strongly depend on the duration of immunity and protection against new variants.

    Sudden rise in COVID-19 MESHD case fatality among young and middle-aged adults in the south of Brazil after identification of the novel B.1.1.28.1 ( P.1 HGNC) SARS-CoV-2 strain: analysis of data from the state of Parana

    Authors: Maria Helena Santos de Oliveira; Giuseppe Lippi; Brandon Michael Henry

    doi:10.1101/2021.03.24.21254046 Date: 2021-03-26 Source: medRxiv

    Brazil is currently suffering a deadly surge of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections MESHD, which has been attributed to the spread of a new strain known as P.1 HGNC (B.1.1.28.1). In this investigation, we analyzed coronavirus disease 2019 MESHD ( COVID-19 MESHD) public health data from Parana, the largest state in southern half of Brazil, between September 1, 2020 and March 17, 2021, to evaluate recent trends in case fatality rates in different age groups. A total of 553,518 cases of SARS-CoV-2, 8,853 currently registered as fatal, were finally included in our analysis. All age groups showed either decline or stabilization of the case fatality rates (CFRs) between September 2020 and January 2021. In February 2021, an increase in CFR for almost all age groups could be instead observed. All groups above 20 years of age showed statistically significant increases in CFR when diagnosed in February 2021 as opposed to January 2021. Patients aged 20-29 years experienced a tripling of their CFR, from 0.04% to 0.13%, while those aged 30-39, 40-49, 50-59 experienced approximate CFR doubling. Individuals between 20 and 29 years of age whose diagnosis was made in February 2021 had an over 3-fold higher risk of death MESHD compared to those diagnosed in January 2021 (Risk Ratio (RR): 3.15 [95%CI: 1.52-6.53], p<0.01), while those aged 30-39, 40-49, 50-59 years experienced 93% (1.93 [95%CI:1.31-2.85], p<0.01), 110% (RR: 2.10 [95%CI:1.62-2.72], p<0.01), and 80% (RR: 1.80 [95%CI:1.50-2.16], p<0.01) increases in risk of death MESHD, respectively. Notably, the observed CFR increase coincided with the second consecutive month of declining number of diagnosed SARS-CoV-2 cases. Taken together, these preliminary findings suggest significant increases in CFR in young and middle-aged adults after identification of a novel SARS-CoV-2 strain circulating in Brazil, and this should raise public health alarms, including the need for more aggressive local and regional public health interventions and faster vaccination.

    Estimating the impact of interventions against COVID-19 MESHD: from lockdown to vaccination

    Authors: James Thompson; Stephen Wattam

    doi:10.1101/2021.03.21.21254049 Date: 2021-03-26 Source: medRxiv

    Coronavirus disease 2019 MESHD ( COVID-19 MESHD) is an infectious disease of humans caused by severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2). Since the first case was identified in China in December 2019 the disease has spread worldwide, leading to an ongoing pandemic. In this article, we present a detailed agent-based model of COVID-19 MESHD in Luxembourg, and use it to estimate the impact, on cases and deaths, of interventions including testing, contact tracing, lockdown, curfew and vaccination. Our model is based on collation, with agents performing activities and moving between locations accordingly. The model is highly heterogeneous, featuring spatial clustering, over 2000 behavioural types and a 10 minute time resolution. The model is validated against COVID-19 MESHD clinical monitoring data collected in Luxembourg in 2020. Our model predicts far fewer cases and deaths MESHD than the equivalent equation-based SEIR model. In particular, with $R_0 = 2.45$, the SEIR model infects 87% of the resident population while our agent-based model results, on average, in only around 23% of the resident population infected. Our simulations suggest that testing and contract tracing reduce cases substantially, but are much less effective at reducing deaths. Lockdowns appear very effective although costly, while the impact of an 11pm-6am curfew is relatively small. When vaccinating against a future outbreak, our results suggest that herd immunity can be achieved at relatively low levels, with substantial levels of protection achieved with only 30% of the population immune. When vaccinating in midst of an outbreak, the challenge is more difficult. In this context, we investigate the impact of vaccine efficacy, capacity, hesitancy and strategy. We conclude that, short of a permanent lockdown, vaccination is by far the most effective way to suppress and ultimately control the spread of COVID-19 MESHD.

    Acute Brain Ischemia MESHD, Infarction and Hemorrhage MESHD in Subjects Dying with or Without Autopsy-Proven Acute Pneumonia MESHD

    Authors: Thomas G Beach; Lucia I Sue; Anthony J Intorcia; Michael J Glass; Jessica E Walker; Richard Arce; Courtney M Nelson; Geidy E Serrano

    doi:10.1101/2021.03.22.21254139 Date: 2021-03-26 Source: medRxiv

    Stroke is one of the most serious complications of Covid-19 MESHD disease but it is still unclear whether stroke MESHD is more common with Covid-19 MESHD pneumonia MESHD as compared to non- Covid-19 MESHD pneumonia MESHD. We investigated the concurrence rate of autopsy-confirmed acute brain ischemia MESHD, acute brain infarction MESHD and acute brain hemorrhage MESHD with autopsy-proven acute non-Covid pneumonia MESHD in consecutive autopsies in the Arizona Study of Aging and Neurodegenerative Disorders MESHD (AZSAND), a longitudinal clinicopathological study of normal aging and neurodegenerative diseases MESHD. Of 691 subjects with a mean age of 83.4 years, acute pneumonia MESHD was histopathologically diagnosed in 343 (49.6%); the concurrence rates for histopathologically-confirmed acute ischemia MESHD, acute infarction MESHD or subacute infarction MESHD was 14% and did not differ between pneumonia MESHD and non-pneumonia MESHD groups while the rates of acute brain hemorrhage MESHD were 1.4% and 2.0% of those with or without acute pneumonia MESHD, respectively. In comparison, in reviews of Covid-19 MESHD publications, reported clinically-determined rates of acute brain infarction MESHD range from 0.5% to 20% while rates of acute brain hemorrhage MESHD range from 0.13% to 2%. In reviews of Covid-19 MESHD autopsy studies, concurrence rates for both acute brain infarction MESHD and acute brain hemorrhage MESHD average about 10%. Covid-19 MESHD pneumonia MESHD and non- Covid-19 MESHD pneumonia MESHD may have similar risks tor concurrent acute brain infarction MESHD and acute brain hemorrhage MESHD when pneumonia MESHD is severe enough to cause death MESHD. Additionally, acute brain ischemia MESHD, infarction MESHD or hemorrhage MESHD may not be more common in subjects dying of acute pneumonia MESHD than in subjects dying without acute pneumonia MESHD.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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