Corpus overview


MeSH Disease

Infections (1083)

Disease (1015)

Death (699)

Coronavirus Infections (631)

Fever (322)

Human Phenotype

Pneumonia (325)

Fever (323)

Hypertension (254)

Cough (250)

Anxiety (129)


age categories (2567)

gender (921)

Transmission (398)

fomite (241)

asymptotic cases (205)

    displaying 21 - 30 records in total 2591
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    Phylogenomic analysis of SARS-CoV-2 genomes from western India reveals unique linked mutations

    Authors: Dhiraj Paul; Kunal Jani; Janesh Kumar; Radha Chauhan; Vasudevan Seshadri; Girdhari Lal; Rajesh Karyakarte; Suvarna Joshi; Murlidhar Tambe; Sourav Sen; Santosh Karade; Kavita Bala Anand; Shelinder Pal Singh Shergill; Rajiv Mohan Gupta; Manoj Kumar Bhat; Arvind Sahu; Yogesh S Shouche

    doi:10.1101/2020.07.30.228460 Date: 2020-07-31 Source: bioRxiv

    India has become the third worst-hit nation by the COVID-19 pandemic caused by the SARS-CoV-2 virus. Here, we investigated the molecular, phylogenomic, and evolutionary dynamics of SARS-CoV-2 in western India, the most affected region of the country. A total of 90 genomes were sequenced. Four nucleotide variants, namely C241T, C3037T, C14408T (Pro4715Leu), and A23403G (Asp614Gly), located at 5UTR, Orf1a, Orf1b, and Spike protein regions of the genome, respectively, were predominant and ubiquitous (90%). Phylogenetic analysis of the genomes revealed four distinct clusters, formed owing to different variants. The major cluster (cluster 4) is distinguished by mutations C313T, C5700A, G28881A are unique patterns and observed in 45% of samples. We thus report a newly emerging pattern of linked mutations. The predominance of these linked mutations suggests that they are likely a part of the viral fitness landscape. A novel and distinct pattern of mutations in the viral strains of each of the districts was observed. The Satara district viral strains showed mutations primarily at the 3' end of the genome, while Nashik district viral strains displayed mutations at the 5' end of the genome. Characterization of Pune strains showed that a novel variant has overtaken the other strains. Examination of the frequency of three mutations i.e., C313T, C5700A, G28881A in symptomatic versus asymptomatic TRANS patients indicated an increased occurrence in symptomatic cases, which is more prominent in females TRANS. The age TRANS-wise specific pattern of mutation is observed. Mutations C18877T, G20326A, G24794T, G25563T, G26152T, and C26735T are found in more than 30% study samples in the age group TRANS of 10-25. Intriguingly, these mutations are not detected in the higher age TRANS range 61-80. These findings portray the prevalence SERO of unique linked mutations in SARS-CoV-2 in western India and their prevalence SERO in symptomatic patients. ImportanceElucidation of the SARS-CoV-2 mutational landscape within a specific geographical location, and its relationship with age TRANS and symptoms, is essential to understand its local transmission TRANS dynamics and control. Here we present the first comprehensive study on genome and mutation pattern analysis of SARS-CoV-2 from the western part of India, the worst affected region by the pandemic. Our analysis revealed three unique linked mutations, which are prevalent in most of the sequences studied. These may serve as a molecular marker to track the spread of this viral variant to different places.

    Changes in the behavioural determinants of health during the coronavirus (COVID-19) pandemic: gender TRANS, socioeconomic and ethnic inequalities in 5 British cohort studies

    Authors: David Bann; Aase Villadsen; Jane Maddock; Alun Hughes; George Ploubidis; Richard Silverwood; Praveetha Patalay

    doi:10.1101/2020.07.29.20164244 Date: 2020-07-31 Source: medRxiv

    Background: The coronavirus (COVID-19) pandemic and consequent physical distancing measures are expected to have far-reaching consequences on population health, particularly in already disadvantaged groups. These consequences include changes in health impacting behaviours (such as exercise, sleep, diet and alcohol use) which are arguably important drivers of health inequalities. We sought to add to the rapidly developing empirical evidence base investigating the impacts of the pandemic on such behavioural outcomes. Methods: Using data from five nationally representative British cohort studies (born 2001, 1990, 1970, 1958, and 1946), we investigated sleep, physical activity (exercise), diet, and alcohol intake (N=14,297). Using measures of each behaviour reported before and during lockdown, we investigated change in each behaviour, and whether such changes differed by age TRANS/cohort, gender TRANS, ethnicity, and socioeconomic position (SEP; childhood social class, education attainment, and adult TRANS reporting of financial difficulties). Binary or ordered logistic regression models were used, adjusting for prior measures of each health behaviour and accounting for study design and non-response weights. Meta-analyses were used to pool cohort-specific estimates and formally test for heterogeneity across cohorts. Results: Changes in these outcomes occurred in in both directions ie, shifts from the middle part of the distribution to both declines and increases in sleep, exercise, and alcohol use. For all outcomes, older cohorts were less likely to report changes in behaviours compared with younger cohorts. In the youngest cohort (born 2001), the following shifts were more evident: increases in exercise, fruit and vegetable intake, sleep, and less frequent alcohol consumption. After adjustment for prior behaviour levels, during lockdown females TRANS were less likely to sleep within the typical range (6-9 hours) yet exercised more frequently; lower SEP was associated with lower odds of sleeping within the typical range (6-9 hours), lower exercise participation, and lower consumption of fruit and vegetables; and ethnic minorities were less likely than White participants to sleep within the typical range (6-9 hours), exercise less frequently, yet reported less frequent alcohol consumption. Conclusions: Our findings highlight the multiple changes to behavioural outcomes that may have occurred due to COVID-19 lockdown, and the differential impacts across generation, gender TRANS, SEP and ethnicity. Such changes require further monitoring given their possible implications to population health and the widening of health inequalities.

    Job insecurity, financial threat and mental health in the COVID-19 context: The buffer role of perceived social support

    Authors: Carlos-Maria Alcover; Sergio Salgado; Gabriela Nazar; Raul Ramirez-Vielma; Carolina Gonzalez-Suhr

    doi:10.1101/2020.07.31.20165910 Date: 2020-07-31 Source: medRxiv

    The social distancing, confinement and quarantine adopted since March 2020 to confront the COVID-19 pandemic have affected multiple vital areas, and specially work, business and productive activities. Prior research has highlighted the relation between perceptions of risk in employment and its concomitant financial risk with a myriad of consequences for people's well-being and health. In order to analyze the potential negative consequences of temporary layoffs, downsizing or closure of companies and businesses, and the consequent insecurity about the continuity of employment, the aim of this study is twofold. Firstly, to analyze the relations between the perceptions of job insecurity and financial threat and overall mental health during the first month of the COVID-19 pandemic in a sample of the Chilean adult TRANS population. And secondly, to identify the potential buffer effect of perceived social support on this relation. To analyze this, we carried out a cross-sectional study on a non-probabilistic sample aimed at a general Chilean adult TRANS population. The results show that both perceptions of job insecurity and financial threat are associated with a decline in perceived mental health. Additionally, results indicate a moderate buffer effect of perceived social support relative to the size of the social network. Thus, in relation to job insecurity and financial threat, the network size mitigates the association of both with the decline in perceived mental health. The theoretical and applied scope of these findings are analyzed, and their challenges and limitations are discussed.

    Regional now- and forecasting for data reported with delay: A case study in COVID-19 infections MESHD

    Authors: Giacomo De Nicola; Marc Schneble; Göran Kauermann; Ursula Berger

    id:2007.16058v1 Date: 2020-07-31 Source: arXiv

    Governments around the world continue to act to contain and mitigate the spread of COVID-19. The rapidly evolving situation compels officials and executives to continuously adapt policies and social distancing measures depending on the current state of the spread of the disease TRANS disease MESHD. In this context, it is crucial for policymakers to have a firm grasp on what the current state of the pandemic is as well as to have an idea of how the infective situation is going to unfold in the next days. However, as in many other situations of compulsorily-notifiable diseases MESHD and beyond, cases are reported with delay to a central register, with this delay deferring an up-to-date view of the state of things. We provide a stable tool for monitoring current infection MESHD levels as well as predicting infection MESHD numbers in the immediate future at the regional level. We accomplish this through nowcasting of cases that have not yet been reported as well as through forecasting of future infections MESHD. The two steps are also combined in forenowcasting. We apply our model to German data, for which our focus lies in explaining and predicting infectious behaviour by district, age group TRANS and gender TRANS.


    Authors: Andrew Crouse; Tiffany Grimes; Peng Li; Matthew Might; Fernando Ovalle; Anath Shalev

    doi:10.1101/2020.07.29.20164020 Date: 2020-07-31 Source: medRxiv

    BACKGROUND: Coronavirus disease MESHD-2019 (COVID-19) is a growing pandemic with an increasing death MESHD toll that has been linked to various comorbidities as well as racial disparity. However, the specific characteristics of these at-risk populations are still not known and approaches to lower mortality are lacking. METHODS: We conducted a retrospective electronic health record data analysis of 25,326 subjects tested for COVID-19 between 2/25/20 and 6/22/20 at the University of Alabama at Birmingham Hospital, a tertiary health care center in the racially diverse Southern U.S. The primary outcome was mortality in COVID-19-positive subjects and the association with subject characteristics and comorbidities was analyzed using simple and multiple linear logistic regression. RESULTS: The odds ratio of contracting COVID-19 was disproportionately high in Blacks/African-Americans (OR 2.6; 95%CI 2.19-3.10; p<0.0001) and in subjects with obesity MESHD obesity HP (OR 1.93; 95%CI 1.64-2.28; p<0.0001), hypertension MESHD hypertension HP (OR 2.46; 95%CI 2.07-2.93; p<0.0001), and diabetes (OR 2.11; 95%CI 1.78-2.48; p<0.0001). Diabetes was also associated with a dramatic increase in mortality (OR 3.62; 95%CI 2.11-6.2; p<0.0001) and emerged as an independent risk factor in this diverse population even after correcting for age TRANS, race, sex, obesity MESHD obesity HP and hypertension MESHD hypertension HP. Interestingly, we found that metformin treatment was independently associated with a significant reduction in mortality in subjects with diabetes and COVID-19 (OR 0.33; 95%CI 0.13-0.84; p=0.0210). CONCLUSION: Thus, these results suggest that while diabetes is an independent risk factor for COVID-19-related mortality, this risk is dramatically reduced in subjects taking metformin, raising the possibility that metformin may provide a protective approach in this high risk population.

    Transmission TRANS of SARS-CoV-2 following exposure in school settings: experience from two Helsinki area exposure incidents.

    Authors: Timothee Dub; Elina Erra; Lotta Hagberg; Emmi Sarvikivi; Camilla Virta; Asko Jarvinen; Pamela Osterlund; Niina Ikonen; Anu Haveri; Merit Melin; Timo J Lukkarinen; Hanna Nohynek

    doi:10.1101/2020.07.20.20156018 Date: 2020-07-30 Source: medRxiv

    Background: The role of children TRANS in SARS-CoV-2 transmission TRANS is unclear. We investigated two COVID-19 school exposure incidents in the Helsinki area. Methods: We conducted two retrospective cohort studies after schools exposures, with a household transmission TRANS extension. We defined a case as an exposed person with either a positive RT-PCR, or positive microneutralisation testing (MNT) as confirmation of SARS-CoV-2 nucleoprotein IgG antibodies SERO detection via fluorescent microsphere immunoassay SERO (FMIA). We recruited close school contacts and families of school cases, calculated attack rates TRANS (AR) on school level and families, and identified transmission chains TRANS. Findings: In incident A, the index was a pupil. Participation rate was 74% (89/121), and no cases were identified. In incident B, the index was a member of school personnel. Participation rate was 81% (51/63). AR was 16% (8/51): 6 pupils and 1 member of school personnel were MNT and FMIA positive; 1 pupil had a positive RT-PCR, but negative serology samples. We visited all school cases' families (n=8). The AR among close household contacts TRANS was 42% (9/20 in 3/8 families) but other plausible sources were always reported. At three months post-exposure, 6/8 school cases were re-sampled and still MNT positive. Interpretation: When the index was a child TRANS, no school transmission TRANS was identified, while the occurrence of an adult TRANS case led to a 16% AR. Further cases were evidenced in 3 families, but other transmission chains TRANS were plausible. It is likely that transmission TRANS from children TRANS to adults TRANS is limited. Funding: The Finnish Institute for Health and Welfare funded this study.

    Use of a humanized anti-CD6 monoclonal antibody SERO (itolizumab) in elderly TRANS patients with moderate COVID-19

    Authors: Mayra Ramos-Suzarte; Yayquier Diaz; Yordanis Martin; Nestor Antonio Calderon; William Santiago; Orlando Vinet; Yulieski La O; Jorge Perez; Augusto Oyarzabal; Yoan Perez; Geidy Lorenzo; Meylan Cepeda; Danay Saavedra; Zayma Mazorra; Daymys Estevez; Patricia Lorenzo-Luaces; Carmen Valenzuela; Armando Caballero; Kalet leon; Tania Crombet; Carlos Jorge Hidalgo

    doi:10.1101/2020.07.24.20153833 Date: 2020-07-30 Source: medRxiv

    Abstract Introduction: The Severe Acute Respiratory Syndrome MESHD Coronavirus 2 (SARS-CoV-2) has caused a recent outbreak of Coronavirus Disease MESHD (COVID-19). In Cuba, the first case of COVID-19 was reported on March 11. Elderly TRANS with multiple comorbidities are particularly susceptible to adverse clinical outcomes in the course of SARS CoV-2 infection MESHD. During the outbreak, a local transmission TRANS event took place in a nursing home in Villa Clara province, Cuba, in which nineteen elderly TRANS residents were positive for SARS-CoV-2. Methods: Based on the increased susceptibility to viral-induced cytokine release syndrome MESHD inducing respiratory and systemic complications in this population, the patients were included in an expanded access clinical trial to receive itolizumab, an anti-CD6 monoclonal antibody SERO. Results: All the patients had underlying medical conditions. The product was well tolerated. After the first dose, the course of the disease MESHD was favorable and 18 out of 19 (94.7%) patients were discharged clinically recovered with negative RT-PCR at 13 days (median). One dose of itolizumab, circulating IL-6 decreased in the first 24-48 hours in patients with high baseline values, whereas in patients with low levels, this concentration remained over low values. To preliminary assess the effect of itolizumab, a control group was selected among the Cuban COVID-19 patients, which did not receive immunomodulatory therapy. Control subjects were well-matched regarding age TRANS, comorbidities and severity of the disease MESHD. Every three moderately ill patients treated with itolizumab, one admission in intensive care unit (ICU) was prevented. Discussion/Conclusion: Itolizumab was well tolerated. Its effect is associated with a reduction and controlling IL-6 serum SERO levels. Moreover, treated patients had a favorable clinical outcome, considering their poor prognosis. This treatment is associated significantly with a decrease the risk to be admitted in ICU and reduced 10 times the risk of death MESHD. This study corroborates that the timely use of itolizumab, in combination with other antiviral and anticoagulant therapies, is associated with a reduction the COVID-19 disease MESHD worsening and mortality. The humanized antibody SERO itolizumab emerges as a therapeutic alternative for patients with COVID-19 and suggests its possible use in patients with cytokine release syndrome MESHD from other pathologies.

    Nicotine-replacement therapy, as a surrogate of smoking, and the risk of hospitalization with Covid-19 and all-cause mortality: a nationwide, observational cohort study in France

    Authors: Mahmoud Zureik; Berangere Baricault; Celementine Vabre; Laura SEMENZATO; Jerome Drouin; Francois cuenot; Laetitia penso; Philippe Herlemont; Emilie Sbidian; Alain Weill; Mathieu Molimard; Rosemary Dray-Spira; Jeremie Botton

    doi:10.1101/2020.07.28.20160630 Date: 2020-07-30 Source: medRxiv

    Abstract Introduction Several studies have reported an unexpectedly low prevalence SERO of current smoking among hospitalized patients with Covid-19. However, these studies mostly compared observed to expected rates of smoking without direct comparison with individual controls. Objective To examine the association of nicotine-replacement therapy, as a surrogate of smoking, with hospitalization and all-cause mortality during the first wave of SARS-CoV-2 epidemic in France. Methods We conducted a nationwide matched exposed/unexposed cohort study using information from the French national health data system which covers the entire French population. We conducted two separate analyses, the first in individuals exposed to nicotine-replacement therapy without major smoking-related diseases MESHD (cancer, cardiovascular and/or respiratory diseases MESHD) and the second in those presenting these conditions. We included all individuals, aged TRANS between 18 and 75 years, who had been reimbursed at least one nicotine-replacement therapy between November 15, 2019, and February 15, 2020. For each exposed individual, we randomly selected, from the entire Metropolitan French population, up to two non-exposed individuals (1:2) matched for the following variables: age TRANS (same year of birth), sex, department of residence (n=96 in Metropolitan France), and complementary universal health insurance (CMU-C). The three end points were a hospitalization with Covid-19, a death MESHD or an intubation in hospitalized patients with Covid-19, and all-cause mortality. We compared outcomes in individuals who were exposed to nicotine-replacement therapy with those in individuals who were not, using a multivariable Cox model with inverse probability weighting according to the propensity score. Results In the first analysis, 297,070 individuals without major smoking-related diseases MESHD exposed to nicotine-replacement therapy were matched with 558,228 unexposed individuals without major smoking-related diseases MESHD. Individuals were aged TRANS on average 45.6 years (standard deviation: 12.7) and 48.8% were male TRANS. From February 15, 2020 to June 7, 2020, hospitalization with Covid-19 occurred in 647 patients (151 patients in the nicotine-replacement therapy group and 496 patients in the unexposed group). In the main multivariable analysis, nicotine-replacement therapy was associated with a decreased risk of hospitalization with Covid-19 compared with unexposed individuals (hazard ratio, 0.50; 95% CI, 0.41 to 0.61). Nicotine-replacement therapy exposure was also associated with a decreased risk of intubation or death MESHD in hospitalized individuals with Covid-19 (13 vs. 73 patients, hazard ratio, 0.31; 95% CI, 0.17 to 0.57) but with an increased risk of all-cause mortality (251 vs. 231 deaths MESHD, hazard ratio, 1.49; 95% CI, 1.24 to 1.80). In the second analysis, 128,768 individuals with major smoking-related diseases MESHD exposed to nicotine-replacement therapy were matched with 243,793 unexposed individuals. Individuals were aged TRANS on average 55.3 years (standard deviation: 11.4) and 53.3% were male TRANS. In the main multivariable analysis, nicotine-replacement therapy exposure was neither associated with risk of hospitalization with Covid-19 (240 patients in the nicotine-replacement therapy group and 398 patients in the unexposed group, hazard ratio, 1.13; 95% CI, 0.94 to 1.38) nor with risk of death MESHD or an intubation in hospitalized individuals with Covid-19 (48 vs. 61 patients, hazard ratio, 1.00; 95% CI, 0.65 to 1.54). All-cause mortality was higher in the nicotine-replacement therapy group (1040 vs. 366 deaths MESHD, hazard ratio, 3.83; 95% CI, 3.41 to 4.31). Conclusions This large-scale observational study suggests that smoking, measured by exposure to nicotine-replacement therapy, was associated with an increased risk of overall mortality during the first wave of SARS-CoV-2 epidemic in France, although it was associated with a lower risk of severe Covid-19 in individuals without major related-smoking diseases MESHD. Experimental and clinical studies are needed to disentangle the potential mechanisms of nicotine and/or smoking in Covid-19 risk. Whatever the nature of these associations, the global impact of smoking is harmful for health even over a short epidemic period.

    Early Clinical Factors Predicting the Development of Critical Disease MESHD in Japanese Patients with COVID-19: A Single-Center Retrospective, Observational Study

    Authors: Takatoshi Higuchi; Tsutomu Nishida; Hiromi Iwahashi; Osamu Morimura; Yasushi Otani; Yukiyoshi Okauchi; Masaru Yokoe; Norihiro Suzuki; Masami Inada; Kinya Abe

    doi:10.1101/2020.07.29.20159442 Date: 2020-07-30 Source: medRxiv

    Background: Insufficient evidence of factors predicting the COVID-19 progression from mild to moderate to critical has been established. We retrospectively evaluated risk factors for critical progression in Japanese COVID-19 patients. Method: Seventy-four laboratory-confirmed COVID-19 patients were hospitalized in our hospital between February 20, 2020, and June 10, 2020. We excluded asymptomatic TRANS, non-Japanese, and child TRANS patients. We divided patients into the stable group (SG) and the progression group (PG) (patients requiring mechanical ventilation). We compared the clinical factors in both groups. We established the cutoff values (COVs) for significantly different factors via receiver operating characteristic (ROC) curve analysis and evaluated risk factors by univariate regression. Results: We enrolled 57 COVID-19 patients (median age TRANS 52 years, 56.1% male TRANS). The median progression time from symptom onset TRANS was eight days. Seven patients developed critical disease MESHD (PG: 12.2%), two (3.5%) of whom died; 50 had stable disease MESHD. Univariate logistic analysis identified elevated lactate dehydrogenase (LDH) (COV: 309 U/l), decreased estimated glomerular filtration rate (eGFR) (COV: 68 ml/min), lymphocytopenia (COV: 980/l), and statin use as significantly associated with disease progression MESHD. However, in Cox proportional hazards analysis, lymphocytopenia at symptom onset TRANS was not significant. Conclusions: We identified three candidate risk factors for adult TRANS Japanese patients with mild to moderate COVID-19: statin use, elevated LDH level, and decreased eGFR.

    Estimates of the rate of infection and asymptomatic MESHD asymptomatic TRANS COVID-19 disease MESHD in a population sample from SE England

    Authors: Philippa M Wells; Katie M Doores; Simon Couvreur; Rocio Martin Martinez; Jeffrey Seow; Carl Graham; Sam Acors; Neophytos Kouphou; Stuart Neil; Richard Tedder; Pedro Matos; Kate Poulton; Maria Jose Lista; Ruth Dickenson; Helin Sertkaya; Thomas Maguire; Edward Scourfield; Ruth Bowyer; Deborah Hart; Aoife O'Byrne; Kathryn Steele; Oliver Hemmings; Carolina Rosadas; Myra McClure; Joan Capedevila-Pujol; Jonathan wolf; Sebastien Ourseilin; Matthew Brown; Michael Malim; Timothy Spector; Claire Steves

    doi:10.1101/2020.07.29.20162701 Date: 2020-07-30 Source: medRxiv

    Background: Understanding of the true asymptomatic TRANS rate of infection MESHD of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence SERO after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms. Methods: We undertook enzyme linked immunosorbent assay SERO characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein of 431 unselected general-population participants of the TwinsUK cohort from South-East England, aged TRANS 19-86 (median age TRANS 48; 85% female TRANS). 382 participants completed prospective logging of 14 COVID-19 related symptoms via the COVID Symptom Study App, allowing consideration of serology alongside individual symptoms, and a predictive algorithm for estimated COVID-19 previously modelled on PCR positive individuals from a dataset of over 2 million. Findings: We demonstrated a seroprevalence SERO of 12% (51participants of 431). Of 48 seropositive individuals with full symptom data, nine (19%) were fully asymptomatic TRANS, and 16 (27%) were asymptomatic TRANS for core COVID-19 symptoms: fever MESHD fever HP, cough MESHD cough HP or anosmia HP. Specificity of anosmia HP for seropositivity was 95%, compared to 88% for fever MESHD fever HP cough MESHD cough HP and anosmia HP combined. 34 individuals in the cohort were predicted to be Covid-19 positive using the App algorithm, and of those, 18 (52%) were seropositive. Interpretation: Seroprevalence SERO amongst adults TRANS from London and South-East England was 12%, and 19% of seropositive individuals with prospective symptom logging were fully asymptomatic TRANS throughout the study. Anosmia HP demonstrated the highest symptom specificity for SARS-CoV-2 antibody SERO response. Funding: NIHR BRC, CDRF, ZOE global LTD, RST-UKRI/MRC

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MeSH Disease
Human Phenotype

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