Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (42)

NSP5 (10)

ProteinN (7)

ComplexRdRp (6)

ProteinE (5)


SARS-CoV-2 Proteins
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    The second wave of COVID-19 MESHD incidence and deaths MESHD in Germany - driven by values, social status and migration background? A county-scale explainable machine learning approach

    Authors: Gabriele Doblhammer; Constantin Reinke; Daniel Kreft

    doi:10.1101/2021.04.14.21255474 Date: 2021-04-14 Source: medRxiv

    There is a general consensus that SARS-CoV-2 infections MESHD and COVID-19 MESHD deaths MESHD have hit lower social groups the hardest, however, for Germany individual level information on socioeco-nomic characteristics of infections and deaths does not exist. The aim of this study was to identify the key features explaining SARS-CoV-2 infections MESHD and COVID-19 MESHD deaths during the upswing of the second wave in Germany. We considered information on COVID-19 MESHD diagnoses and deaths from 1. October to 15. De-cember 2021 on the county-level, differentiating five two-week time periods. We used 155 indicators to characterize counties in nine geographic, social, demographic, and health do-mains. For each period, we calculated directly age-standardized COVID-19 MESHD incidence and death MESHD rates on the county level. We trained gradient boosting models to predict the inci-dence and death rates with the 155 characteristics of the counties for each period. To ex-plore the importance and the direction of the correlation of the regional indicators we used the SHAP HGNC procedure. We categorized the top 20 associations identified by the Shapley values into twelve categories depicting the correlation between the feature and the outcome. We found that counties with low SES were important drivers in the second wave, as were those with high international migration and a high proportion of foreigners and a large nurs-ing home population. During the period of intense exponential increase in infections, the proportion of the population that voted for the Alternative for Germany (AfD) party in the last federal election was among the top characteristics correlated with high incidence and death MESHD rates. We concluded that risky working conditions with reduced opportunities for social distancing and a high chronic disease burden put populations in low-SES counties at higher risk of SARS-CoV-2 infections MESHD and COVID-19 MESHD deaths. In addition, noncompliance with Corona measures and spill-over effects from neighbouring counties increased the spread of the virus. To fur-ther substantiate this finding, we urgently need more data at the individual level.

    Case fatality rates for COVID-19 MESHD are higher than case fatality rates for motor vehicle accidents for individuals over 40 years of age

    Authors: Arjun Puranik; Michiel J.M. Niesen; Emily Lindemer; Patrick Lenehan; Tudor Cristea-Platon; Colin Pawlowski; Venky Soundararajan

    doi:10.1101/2021.04.09.21255193 Date: 2021-04-13 Source: medRxiv

    The death toll of the COVID-19 pandemic MESHD has been unprecedented, due to both the high number of SARS-CoV-2 infections MESHD SARS-CoV-2 infections MESHD and the seriousness of the disease resulting from these infections. Here, we present mortality rates and case fatality rates for COVID-19 MESHD over the past year compared with other historic leading causes of death MESHD in the United States. Among the risk categories considered, COVID-19 MESHD is the third leading cause of death MESHD for individuals 40 years old and over, with an overall annual mortality rate of 325 deaths MESHD per 100K individuals, behind only cancer MESHD (385 deaths per 100K individuals) and heart disease MESHD (412 deaths per 100K individuals). In addition, for individuals 40 years old and over, the case fatality rate for COVID-19 MESHD is greater than the case fatality rate for motor vehicle accidents. In particular, for the age group 40-49, the relative case fatality rate of COVID-19 MESHD is 1.5 fold (95% CI: [1.3, 1.7]) that of a motor vehicle accident, demonstrating that SARS-CoV-2 infection MESHD may be significantly more dangerous than a car crash for this age group. For older adults, COVID-19 MESHD is even more dangerous, and the relative case fatality rate of COVID-19 MESHD is 29.4 fold (95% CI: [23.2, 35.7]) that of a motor vehicle accident for individuals over 80 years old. On the other hand, motor vehicle accidents have a 4.5 fold (95% CI: [3.9, 5.1]) greater relative case fatality rate compared to COVID-19 MESHD for the age group of 20-29 years. These results highlight the severity of the COVID-19 pandemic MESHD especially for adults above 40 years of age and underscore the need for large-scale preventative measures to mitigate risks for these populations. Given that FDA-authorized COVID-19 MESHD vaccines have now been validated by multiple studies for their outstanding real-world effectiveness and safety, vaccination of all individuals who are over 40 years of age is one of the most pressing public health priorities of our time.

    High coverage COVID-19 MESHD mRNA vaccination rapidly controls SARS-CoV-2 transmission in Long-Term Care Facilities

    Authors: Pablo Martinez de Salazar; Nicholas Link; Karuna Lamarca; Mauricio Santillana

    doi:10.1101/2021.04.08.21255108 Date: 2021-04-13 Source: medRxiv

    Residents of Long-Term Care Facilities (LTCFs) represent a major share of COVID-19 MESHD deaths worldwide. Information on vaccine effectiveness in these settings is essential to improve mitigation strategies, but evidence remains limited. To evaluate the early effect of the administration of BNT162b2 mRNA vaccines in LTCFs, we monitored subsequent SARS-CoV-2 documented infections and deaths in Catalonia MESHD, a region of Spain, and compared them to counterfactual model predictions from February 6th to March 28th, 2021, the subsequent time period after which 70% of residents were fully vaccinated. We calculated the reduction in SARS-CoV-2 documented infections and deaths MESHD as well as the detected county-level transmission. We estimated that once more than 70% of the LTCFs population were fully vaccinated, 74% (58%-81%, 90% CI) of COVID-19 MESHD deaths MESHD and 75% (36%-86%) of all documented infections were prevented. Further, detectable transmission was reduced up to 90% (76-93% 90%CI). Our findings provide evidence that high-coverage vaccination is the most effective intervention to prevent SARS-CoV-2 transmission and death MESHD. Widespread vaccination could be a feasible avenue to control the COVID-19 pandemic MESHD.

    Nosocomial Pseudomonas aeruginosaregulates alginate biosynthesis and Type VI secretion system during adaptive and convergent evolution for coinfection in critically ill COVID-19 MESHD patients

    Authors: Zhao Cai; Xiangke Duan; Han Zhang; Shuhong Han; Kaiwei Yu; Yingdan Zhang; Yang Liu; Liang Yang

    doi:10.1101/2021.04.09.439260 Date: 2021-04-11 Source: bioRxiv

    COVID-19 pandemic MESHD has caused millions of death MESHD globally and caused huge impact on the health of infected MESHD patients. Shift in the lung microbial ecology upon such viral infection often worsens the disease MESHD and increases host susceptibility to secondary infections. Recent studies have indicated that bacterial coinfection is an unignorable factor contributing to the aggravation of COVID-19 MESHD and posing great challenge to clinical treatments. However, there is still a lack of in-depth investigation on the coinfecting bacteria in COVID-19 MESHD patients for better treatment of bacterial coinfection. With the knowledge that Pseudomonas aeruginosa is one of the top coinfecting pathogens, we analyzed the adaptation and convergent evolution of nosocomial Pseudomonas aeruginosa isolated from two critical COVID-19 MESHD patients in this study. We sequenced and compared the genomes and transcriptomes of Pseudomonas aeruginosa isolates longitudinally and parallelly for its evolutionary traits. Pseudomonas aeruginosa overexpressed alginate and attenuated Type VI secretion system MESHD (T6SS) during coinfection for excessive biofilm formation and suppressed virulence. Results of bacterial competition assay and macrophage cytotoxicity MESHD test indicated that Pseudomonas aeruginosa reduced its virulence towards both prokaryotic competitors and eukaryotic host through inhibiting its T6SS during evolution. Pseudomonas aeruginosa T6SS is thus one of the reasons for its advantage to cause coinfection in COVID-19 MESHD patients while the attenuation of T6SS could cause a shift in the microecological composition in the lung. Our study will contribute to the development of therapeutic measures and the discovery of novel drug target to eliminate Pseudomonas aeruginosa coinfection MESHD in COVID-19 MESHD patient.

    Covid-19 MESHD and Excess Mortality in Medicare Beneficiaries

    Authors: Scott D Greenwald; Nassib G Chamoun; Paul J Manberg; Josh Gray; David Clain; Kamal Maheshwari; Daniel I Sessler

    doi:10.1101/2021.04.07.21254793 Date: 2021-04-10 Source: medRxiv

    We estimated excess mortality in Medicare recipients with probable and confirmed Covid-19 MESHD infections in the general community and amongst residents of long-term care (LTC) facilities. We considered 28,389,098 Medicare and dual-eligible recipients from one year before February 29, 2020 through September 30, 2020, with mortality followed through November 30th, 2020. Probable and confirmed Covid-19 MESHD diagnoses, presumably mostly symptomatic, were determined from ICD-10 codes. We developed a Risk Stratification Index (RSI) mortality model which was applied prospectively to establish baseline mortality risk. Excess deaths MESHD attributable to Covid-19 MESHD were estimated by comparing actual-to-expected deaths based on historical comparisons and in closely matched cohorts with and without Covid-19 MESHD. 677,100 (2.4%) beneficiaries had confirmed Covid-19 MESHD and 2,917,604 (10.3%) had probable Covid-19 MESHD. 472,329 confirmed cases were community living and 204,771 were in LTC. Mortality following a probable or confirmed diagnosis in the community increased from an expected incidence of about 4% to actual incidence of 7.5%. In long-term care facilities, the corresponding increase was from 20.3% to 24.6%. The absolute increase was therefore similar at 3-4% in the community and in LTC residents. The percentage increase was far greater in the community (89%) than among patients in chronic care facilities (21%) who had higher baseline risk. The LTC population without probable or confirmed Covid-19 MESHD diagnoses experienced 38,932 excess deaths MESHD (35%) compared to historical estimates. Limitations in access to Covid-19 MESHD testing and disease under-reporting in LTC patients probably were important factors, although social isolation and disruption in usual care presumably also contributed. Remarkably, there were 31,360 fewer deaths than expected in community dwellers without probable or confirmed Covid-19 MESHD diagnoses, representing a 6% reduction. Disruptions to the healthcare system and avoided medical care were thus apparently offset by other factors, representing overall benefit. The Covid-19 pandemic MESHD had marked effects on mortality, but the effects were highly context-dependent.

    Modelling the impact of extending dose intervals for COVID-19 MESHD vaccines in Canada

    Authors: Austin Nam; Raphael Ximenes; Man Wah Yeung; Sharmistha Mishra; Jianhong Wu; Matthew Tunis; Beate Sander

    doi:10.1101/2021.04.07.21255094 Date: 2021-04-10 Source: medRxiv

    Background: Dual dose SARS-CoV-2 vaccines demonstrate high efficacy and will be critical in public health efforts to mitigate the COVID-19 pandemic MESHD and its health consequences; however, many jurisdictions face very constrained vaccine supply. We examined the impacts of extending the interval between two doses of mRNA vaccines in Canada in order to inform deliberations of Canada's National Advisory Committee on Immunization. Methods: We developed an age-stratified, deterministic, compartmental model of SARS-CoV-2 transmission and disease to reproduce the epidemiologic features of the epidemic in Canada. Simulated vaccination comprised mRNA vaccines with explicit examination of effectiveness against disease (67% [first dose], 94% [second dose]), hospitalization (80% [first dose], 96% [second dose]), and death MESHD (85% [first dose], 96% [second dose]) in adults aged 20 years and older. Effectiveness against infection was assumed to be 90% relative to the effectiveness against disease. We used a 6-week mRNA dose interval as our base case (consistent with early program rollout across Canadian and international jurisdictions) and compared extended intervals of 12 weeks, 16 weeks, and 24 weeks. We began vaccinations on January 1, 2021 and simulated a third wave beginning on April 1, 2021. Results: Extending mRNA dose intervals were projected to result in 12.1-18.9% fewer symptomatic cases, 9.5-13.5% fewer hospitalizations, and 7.5-9.7% fewer deaths in the population over a 12-month time horizon. The largest reductions in hospitalizations and deaths were observed in the longest interval of 24 weeks, though benefits were diminishing as intervals extended. Benefits of extended intervals stemmed largely from the ability to accelerate coverage in individuals aged 20-74 years as older individuals were already prioritized for early vaccination. Conditions under which mRNA dose extensions led to worse outcomes included: first-dose effectiveness < 65% against death; or protection following first dose waning to 0% by month three before the scheduled 2nd dose at 24-weeks. Probabilistic simulations from a range of likely vaccine effectiveness values did not result in worse outcomes with extended intervals. Conclusion: Under real-world effectiveness conditions, our results support a strategy of extending mRNA dose intervals across all age groups to minimize symptomatic cases, hospitalizations, and deaths MESHD while vaccine supply is constrained.

    TCA-soluble blood serum proteins of COVID-19 MESHD patients as possible predictive markers for the disease severity

    Authors: Andrii Orfin; Tamila Alexanyan; Svitlana Tkachuk Svitlana Tkachuk; Anatoliy Starodub; Taras Luchyshyn; Andriy Sibirny; Serhiy Souchelnytskyi; Yuriy Kit

    doi:10.1101/2021.04.07.21255063 Date: 2021-04-09 Source: medRxiv

    Coronavirus disease MESHD 19 ( COVID-19 MESHD) is a global health crisis on a planetary scale. COVID-19 MESHD in many people has mild or moderate manifestation, although significant number of people, especially the elderly, suffer heavy from this illness, which often resulting in death MESHD. There are reports of similarities in immune response between COVID-19 MESHD and some autoimmune diseases MESHD. Earlier, we have demonstrated that fraction of TCA-soluble blood serum proteins containing a 48 kDA fragment of unconvential Myosin C1 have linked with development of multiple sclerosis MESHD and rheumatoid arthritis MESHD. Here we analyze use of these proteins in determining the severity of disease in COVID-19 MESHD patients. We found that blood serum of COVID-19 MESHD patients in acute disease MESHD manifestation contains, in contrast to healthy individuals, the TCA-soluble proteins with molecular masses 48 kDa and 76 kDA which were identified as a short form of unconventional myosin 1c and a modified form of human serum albumin HGNC.

    The statistical analysis of daily data associated with different parameters of the New Coronavirus COVID-19 pandemic MESHD in Georgia and their short-term interval prediction from September 2020 to February 2021

    Authors: Avtandil G. Amiranashvili; Ketevan R. Khazaradze; Nino D. Japaridze

    doi:10.1101/2021.04.01.21254448 Date: 2021-04-07 Source: medRxiv

    In the autumn - winter period of 2020, very difficult situation arose in Georgia with the course of the pandemic of the New Coronavirus COVID-19 MESHD. In particular, in November-December period of 2020, Georgia eight days was rank a first in the world in terms of COVID-19 MESHD infection rate per 1 HGNC million populations. In this work results of a statistical analysis of the daily data associated with New Coronavirus COVID-19 MESHD infection of confirmed (C), recovered (R), deaths MESHD (D) and infection rate (I) cases of the population of Georgia in the period from September 01, 2020 to February 28, 2021 (for I - from December 05, 2020 to February 28, 2021) are presented. It also presents the results of the analysis of ten-day (decade) and two-week forecasting of the values of C, D and I, the information was regularly sent to the National Center for Disease Control & Public Health of Georgia and posted on the Facebook page The analysis of data is carried out with the use of the standard statistical analysis methods of random events and methods of mathematical statistics for the non-accidental time-series of observations. In particular, the following results were obtained. Georgia's ranking in the world for Covid-19 MESHD infection and deaths from September 1, 2020 to February 28, 2021 ( per 1 HGNC million population) was determined. Georgia was in the first place: Infection - November 21, 22, 27, 28 and December 04, 05, 06, 09, 2020; Death - November 22, 2020. A comparison between the daily mortality from Covid-19 MESHD in Georgia from September 1, 2020 to February 28, 2021 with the average daily mortality rate in 2015-2019 was made. The largest share value of D from mean death in 2015-2019 was 36.9% (19.12.2020), the smallest - 0.9% (21.09.2020, 24.09.2020 - 26.09.2020). The statistical analysis of the daily and decade data associated with coronavirus COVID-19 pandemic MESHD of confirmed, recovered, deaths cases and infection rate of the population of Georgia are carried out. Maximum daily values of investigation parameters are following: C = 5450 (05.12.2020), R = 4599 (21.12.2020), D = 53 (19.12.2020), I = 30.1 % (05.12.2020). Maximum mean decade values of investigation parameters are following: C = 4337 (1 Decade of December 2020), R = 3605 (3 Decade of November 2020), D = 44 (2 Decade of December 2020), I = 26.8 % (1 Decade of December 2020). It was found that the regression equations for the time variability of the daily values of C, R and D have the form of a tenth order polynomial. Mean values of speed of change of confirmed -V(C), recovered - V(R) and deaths - V(D) coronavirus-related cases in different decades of months from September 2020 to February 2021 were determined. Maximum mean decade values of investigation parameters are following: V(C) = +104 cases/day (1 Decade of November 2020), V(R) = +94 cases/day (3 Decade of October and 1 Decade of November 2020), V(D) = +0.9 cases/day (1 Decade of November 2020). Cross-correlations analysis between confirmed COVID-19 MESHD cases with recovered and deaths MESHD cases from 05.12.2020 to 28.02.2021 is carried out. So, the maximum effect of recovery is observed 13-14 days after infection, and deaths - after 13-14 and 17-18 days. The scale of comparing real data with the predicted ones and assessing the stability of the time series of observations in the forecast period in relation to the pre-predicted one was offered. Comparison of real and calculated predictions data of C (23.09.2020-28.02.2021), D (01.01.2021-28.02.2021) and I (01.02.2021-28.02.2021) in Georgia are carried out. It was found that daily, mean decade and two-week real values of C, D and I practically falls into the 67% - 99.99% confidence interval of these predicted values for the specified time periods (except the forecast of C for 13.10.2020-22.10.2020, when a nonlinear process of growth of C values was observed and its real values have exceeded 99.99% of the upper level of the confidence interval of forecast). Alarming deterioration with the spread of coronavirus parameters may arise when their daily values are higher 99.99% of upper level of the forecast confidence interval. Excellent improvement - when these daily values are below 99.99% of the lower level of the forecast confidence interval. The lockdown introduced in Georgia on November 28, 2020 brought positive results. There are clearly positive tendencies in the spread of COVID-19 MESHD to February 2021. Key words: New Coronavirus COVID-19 MESHD, statistical analysis, short-term prediction.

    Social and Clinical Determinants of COVID-19 MESHD Outcomes: Modeling Real-World Data from a Pandemic Epicenter

    Authors: Jyothi Manohar; Sajjad Abedian; Rachel Martini; Scott Kulm; Kaylee Ho; Paul Christos; Mirella Salvatore; Thomas R Campion; Julianne Imperato-McGinley; Said Ibrahim; Teresa H Evering; Erica Phillips; Rulla Tamimi; Vivian Bea; Onyinye Balogun; Andrea Sboner; Olivier Elemento; Melissa Boneta Davis

    doi:10.1101/2021.04.06.21254728 Date: 2021-04-07 Source: medRxiv

    IMPORTANCE: As the United States continues to accumulate COVID-19 MESHD cases and deaths, and disparities persist, defining the impact of risk factors for poor outcomes across patient groups is imperative. OBJECTIVE: Our objective is to use real-world healthcare data to quantify the impact of demographic, clinical, and social determinants of health associated with severe COVID-19 MESHD outcomes. We sought to identify high-risk scenarios and characterize dynamics of risk among racial and ethnic groups. DESIGN: A retrospective cohort of COVID-19 MESHD patients diagnosed between March 1 HGNC and August 20, 2020. Fully adjusted logistical regression models for hospitalization, severe disease and mortality outcomes across 1-the entire cohort and 2- nested within self-reported race/ethnicity groups. SETTING: Three NewYork-Presbyterian health care system that draw patients across all five boroughs of New York City. Data was obtained through automated abstraction of real-world data from electronic medical records. PARTICIPANTS: During the study timeframe, 110,498 individuals were tested for SARS-CoV-2 in the NewYork-Presbyterian health care system; 11,930 patients were confirmed for COVID-19 MESHD by RT-PCR or covid-19 MESHD clinical diagnosis. MAIN OUTCOMES AND MEASURES: The primary predictor of interest was patient race/ethnicity, and study covariates included demographics, clinical comorbidity, and zip HGNC code-based neighborhood socio-economic status. The primary outcomes of interest were COVID-19 MESHD hospitalization, severe disease, and death MESHD. RESULTS: Of the patients who tested positive for COVID-19 MESHD, 4,895 were hospitalized; of those, 1,070 developed severe disease. 1,654 patients suffered COVID-19 MESHD related death. Certain risk factors only showed an impact in specific race groups and varied among outcome models. Clinical factors were more significant than demographic or social determinants. In our all-patients models, hypertension MESHD conveyed the highest risk of hospitalization (OR=1.89, 89p=1.26x10 -1020), while Type 2 Diabetes MESHD was significantly associated with all three outcomes (hospitalization: OR=1.4848, p=1.39x10-04394; severe disease: OR=1.466, p=44.47x10-099; mortality: OR=1.27, p=0.001). In race-nested models, COPD increased risk of hospitalization only in Non-Hispanic (NH)-White patients (OR=2.707, p=0.009). Obesity (BMI 30+) was associated with severe disease among hospitalized NH-White (OR=1.48, p=0.038) and NH-Black (OR=1.77, p=0.025). Cancer MESHD was the only significant mortality risk factor in Hispanic patients (OR=1.9797, p=0.04343), and heart failure MESHD was associated with mortality only in NH-Asian patients (OR=2.62, p=0.001). CONCLUSIONS AND RELEVANCE. We found that clinical comorbidity, more than social determinants, was associated with COVID-19 MESHD outcomes, suggesting clinical factors are more predictive of risk than social factors.

    Comparing between survived and deceased patients with Diabetes Mellitus MESHD and COVID-19 MESHD in Bangladesh: A cross- sectional study from COVID-19 MESHD dedicated hospital

    Authors: Md. Shahed Morshed; Abdullah Al Mosabbir; Mohammad Sorowar Hossain

    doi:10.1101/2021.04.04.21254884 Date: 2021-04-07 Source: medRxiv

    The current coronavirus disease 2019 MESHD ( COVID-19 MESHD) outbreak was reported to cause significantly higher mortality and morbidity among patients with diabetes mellitus MESHD ( DM MESHD). Although Bangladesh is amongst the top 10 countries with diabetic people MESHD, data on these patients with COVID-19 MESHD is scarce from this region. This study aimed to illustrate the clinical features and outcomes of hospitalized patients with COVID-19 MESHD and DM MESHD in Bangladesh while comparing survivors and deceased. This retrospective cross-sectional study was conducted among RT-PCR confirmed COVID-19 MESHD patients with pre-existing Diabetes Mellitus MESHD in a specialized COVID-19 MESHD hospital in Bangladesh. Data from hospital records were analyzed. Among 921 RT-PCR confirmed COVID-19 MESHD admitted during the study period, 231 (~25%) patients with pre-existing DM MESHD (median age 60 years) were included in the analysis. The death rate among all hospitalized patients (with and without DM MESHD) was 2.8% compared to 11.3% among diabetic MESHD patients. The median hospital stay was 13 days (IQR 10.5, 17.0) for survivors and five days (IQR 2.0-8.3) for the deceased. The clinical features were not significantly different between survivors and the deceased. However, deceased patients had significantly lower blood oxygen level (85% vs 93%, p <0.001), and higher neutrophil-lymphocyte ratio (7.9 vs 4.5, p 0.003) and serum ferritin (946.0 vs 425.0 ng/ml, p 0.03). Glycemic status was poor in both groups. This study would help identify a subgroup of diabetic MESHD patients with COVID-19 MESHD who are at higher risk of in-hospital death MESHD and improve clinical decision making.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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