Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
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    Interactions between SARS-CoV-2 and Influenza and the impact of coinfection on disease severity: A test negative design

    Authors: Julia Stowe; Elise Tessier; Hongxin Zhao; Rebecca Guy; Berit Muller-Pebody; Maria Zambon; Nick Andrews; Mary Ramsay; Jamie Lopez Bernal; Jonathan Josephs-Spaulding; Philipp Koehler; Axel Kuenstner; Elisa Rosati; Anna C. Aschenbrenner; Petra Bacher; Nathan Baran; Teide Boysen; Burkhard Brandt; Niklas Bruse; Jonathan Doerr; Andreas Draeger; Gunnar Elke; David Ellinghaus; Julia Fischer; Michael Forster; Andre Franke; Soeren Franzenburg; Norbert Frey; Anette Friedrichs; Janina Fuss; Andreas Glueck; Jacob Hamm; Finn Hinrichsen; Marc P. Hoeppner; Simon Imm; Ralf Juenker; Sina Kaiser; Ying H. Kan; Rainer Knoll; Christoph Lange; Georg Laue; Clemes Lier; Matthias Lindner; Georgios Marinos; Robert Markewitz; Jacob Nattermann; Rainer Noth; Peter Pickkers; Klaus F. Rabe; Alina Renz; Christoph Roecken; Jan Rupp; Annika Schaffarzyk; Alexander Scheffold; Jonas Schulte-Schrepping; Domagoj Schunck; Dirk Skowasch; Thomas Ulas; Klaus-Peter Wandinger; Michael Wittig; Johannes Zimmermann; Hauke Busch; Bimba F. Hoyer; Christoph Kaleta; Jan Heyckendorf; Matthijs Kox; Jan Rybniker; Stefan Schreiber; Joachim Schultze; Philip Rosenstiel; - HCA Lung Biological Network; - Deutsche COVID-19 Omics Initiative (DeCOI)

    doi:10.1101/2020.09.18.20189647 Date: 2020-09-18 Source: medRxiv

    Background: The potential impact of COVID-19 alongside influenza on morbidity, mortality and health service capacity is a major concern as the Northern Hemisphere winter approaches. This study investigates the interaction between influenza and COVID-19 during the latter part of the 2019-20 influenza season in England. Methods: Individuals tested for influenza and SARS-CoV-2 were extracted from national surveillance systems between 20/01/2020 and 25/04/2020. To estimate influenza infection on the risk TRANS infection on the risk TRANS of SARS-CoV-2 infection MESHD, univariable and multivariable analyses on the odds of SARS-CoV-2 in those who tested positive for influenza compared to those who tested negative for influenza. To assess whether a coinfection was associated with severe SARS-CoV-2 outcome, univariable and multivariable analyses on the odds of death MESHD adjusted for age TRANS, sex, ethnicity, comorbidity and coinfection status. Findings: The risk of testing positive for SARS-CoV-2 was 68% lower among influenza positive cases, suggesting possible pathogenic competition between the two viruses. Patients with a coinfection had a risk of death of 5.92 (95% CI, 3.21-10.91) times greater than among those with neither influenza nor SARS-CoV-2 suggesting possible synergistic effects in coinfected individuals. The odds of ventilator use or death MESHD and ICU admission or death MESHD was greatest among coinfection MESHD patients showing strong evidence of an interaction effect compared to SARS-CoV-2/influenza acting independently. Interpretation: Cocirculation of these viruses could have a significant impact on morbidity, mortality and health service demand. Testing for influenza alongside SARS-CoV-2 and maximising influenza vaccine uptake should be prioritised to mitigate these risks.

    Clinical characteristics and outcome of influenza virus infection MESHD among adults TRANS hospitalized with severe COVID-19: A retrospective cohort study from Wuhan, China

    Authors: Xunliang Tong; Xiaomao Xu; Guoyue Lv; He Wang; Anqi Cheng; Dingyi Wang; Yue Zhang; Yanming Li

    doi:10.21203/rs.3.rs-50577/v1 Date: 2020-07-29 Source: ResearchSquare

    Background Coronavirus disease MESHD 2019 (COVID-19) is an emerging infection disease MESHD that rapidly spreads worldwide. Co-infection MESHD may occur in some cases of COVID-19, like influenza virus and so on. Clinical features and outcomes of severe COVID-19 patients with co-infection MESHD of influenza virus need to be noticed.Methods Retrospective cohort study was performed and total of 140 patients with severe COVID-19 was enrolled in designated wards of Sino-French New City Branch of Tongji Hospital between Feb 8th and March 15th in Wuhan, Hubei province, China. The demographic, clinical features, laboratory indices, treatment and outcomes of these patients were collected and analyzed.Results Of 140 severe COVID-19 hospitalized patients, 73 patients were with median age TRANS of 66 years old with identification of influenza virus IgM-positive and 67 patients were with median age TRANS of 62 years old in influenza virus IgM-negative. Nearly half of severe COVID-19 patients in this research are male TRANS. Majority of the severe COVID-19 patients had chronic underlying conditions. Wheeze HP was the clinical feature of severe COVID-19 patients with influenza IgM-positive (26.4% vs 9.0%, P = 0.008). On contrary, fatigue HP fatigue MESHD or myalgia HP myalgia MESHD was the feature of the COVID-19 patients without IgM-positive (38.4% vs 58.2%, P = 0.019). Increased levels of ferritin and prolonging APTT were showed in severe COVID-19 patients without influenza IgM-positive compared with patients in other group with significant differences. Death rate in the group of severe COVID-19 patients with influenza IgM-positive is lower than it in other group with significant differences (4.1% vs 14.9%, P = 0.040). In univariate regression analysis, several factors were associated with higher risk of death MESHD, which included LDH, troponin, NT-proBNP, D-dimer, PT, APTT, lymphocytes, platelet and eGFR. However, influenza virus IgM positive was associated with lower risk of death.Conclusions Characteristic features of patients with severe COVID-19 with influenza virus IgM-positive were described. Co-infection MESHD may occur during the pandemic of COVID-19, and we need to improve our understanding in order to confront this crisis in the future.

    State-level tracking of COVID-19 in the United States

    Authors: H Juliette T Unwin; Swapnil Mishra; Valerie C Bradley; Axel Gandy; Thomas A Mellan; Helen Coupland; Jonathan Ish-Horowicz; Michaela Andrea Christine Vollmer; Charles Whittaker; Sarah L Filippi; Xiaoyue Xi; Mélodie Monod; Oliver Ratmann; Michael Hutchinson; Fabian Valka; Harrison Zhu; Iwona Hawryluk; Philip Milton; Kylie E C Ainslie; Marc Baguelin; Adhiratha Boonyasiri; Nick F Brazeau; Lorenzo Cattarino; Zulma M Cucunubá; Gina Cuomo-Dannenburg; Ilaria Dorigatti; Oliver D Eales; Jeffrey W Eaton; Sabinee L van Elsland; Richard G FitzJohn; Katy A M Gaythorpe; William Green; Wes Hinsley; Benjamin Jeffrey; Edward Knock; Daniel J Laydon; John Lees; Gemma Nedjati-Gilani; Pierre Nouvellet; Lucy C Okell; Kris V Parag; Igor Siveroni; Hayley A Thompson; Patrick Walker; Caroline E Walters; Oliver J Watson; Lilith K Whittles; Azra Ghani; Neil M Ferguson; Steven Riley; Christl A. Donnelly; Samir Bhatt; Seth Flaxman

    doi:10.1101/2020.07.13.20152355 Date: 2020-07-14 Source: medRxiv

    As of 1st June 2020, the US Centers for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths MESHD reported in the next most severely impacted country. We jointly modelled the US epidemic at the state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate the number of individuals that have been infected, the number of individuals that are currently infectious and the time-varying reproduction number TRANS (the average number of secondary infections TRANS secondary infections MESHD caused by an infected person). We used changes in mobility to capture the impact that non-pharmaceutical interventions and other behaviour changes have on the rate of transmission TRANS of SARS-CoV-2. Nationally, we estimated 3.7% [3.4%-4.0%] of the population had been infected by 1st June 2020, with wide variation between states, and approximately 0.01% of the population was infectious. We also demonstrated that good model forecasts of deaths for the next 3 weeks with low error MESHD and good coverage of our credible intervals.

    Characterization of Microbial Co-infections MESHD infections in the Respiratory Tract HP of hospitalized COVID-19 patients

    Authors: Huanzi Zhong; Yanqun Wang; Zhun Shi; Lu Zhang; Huahui Ren; Weiqun He; Zhaoyong Zhang; Airu Zhu; Jingxian Zhao; Fei Xiao; Fangming Yang; Tianzhu Liang; Feng Ye; Bei Zhong; Shicong Ruan; Mian Gan; Jiahui Zhu; Fang Li; Fuqiang Li; Daxi Wang; Jiandong Li; Peidi Ren; Shida Zhu; Huanming Yang; Jian Wang; Karsten Kristiansen; Hein M Tun; Weijun Chen; Nanshan Zhong; Xun Xu; Yi-min Li; Junhua LI; Jincun Zhao

    doi:10.1101/2020.07.02.20143032 Date: 2020-07-05 Source: medRxiv

    Summary Background Severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) has caused a global pandemic of Coronavirus disease MESHD 2019 (COVID-19). However, microbial composition of the respiratory tract and other infected tissues, as well as their possible pathogenic contributions to varying degrees of disease severity in COVID-19 patients remain unclear. Method Between January 27 and February 26, 2020, serial clinical specimens (sputum, nasal and throat swab, anal swab and feces) were collected from a cohort of hospitalized COVID-19 patients, including 8 mildly and 15 severely ill patients (requiring ICU admission and mechanical ventilation), in the Guangdong province, China. Total RNA was extracted and ultra-deep metatranscriptomic sequencing was performed in combination with laboratory diagnostic assays. Co-infection MESHD rates, the prevalence SERO and abundance of microbial communities in these COVID-19 patients were determined. Findings Notably, respiratory microbial co-infections MESHD were exclusively found in 84.6% of severely ill patients (11/13), among which viral and bacterial co-infections MESHD were detected by sequencing in 30.8% (4/13) and 69.2% (9/13) of the patients, respectively. In addition, for 23.1% (3/13) of the patients, bacterial co-infections MESHD with Burkholderia cepacia complex (BCC) and Staphylococcus epidermidis MESHD were also confirmed by bacterial culture. Further, a time-dependent, secondary infection of B. cenocepacia with expressions of multiple virulence genes in one severely ill patient was demonstrated, which might be the primary cause of his disease deterioration and death MESHD one month after ICU admission. Interpretation Our findings identified distinct patterns of co-infections MESHD with SARS-CoV-2 and various respiratory pathogenic microbes in hospitalized COVID-19 patients in relation to disease severity. Detection and tracking of BCC-associated nosocomial infections MESHD are recommended to improve the pre-emptive treatment regimen and reduce fatal outcomes of hospitalized patients infected with SARS-CoV-2. Funding National Science and Technology Major Project of China, National Major Project for Control and Prevention of Infectious Disease MESHD in China, the emergency grants for prevention and control of SARS-CoV-2 of Ministry of Science and Technology and Guangdong province, Guangdong Provincial Key Laboratory of Genome Read and Write, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, and Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics.

    HIV MESHD and risk of COVID-19 death: a population cohort study from the Western Cape Province, South Africa.

    Authors: - Western Cape Department of Health with National Institute for Communicable Diseases, South Africa; Mary-Ann Davies

    doi:10.1101/2020.07.02.20145185 Date: 2020-07-03 Source: medRxiv

    Background: The effect of HIV co-infection MESHD on COVID-19 outcomes in sub-Saharan Africa is unknown. Methods: We conducted a population cohort study using linked data from adults TRANS attending public sector health facilities in the Western Cape, South Africa. We used Cox-proportional hazards models adjusted for age TRANS, sex, location and comorbidities to examine the association between HIV and COVID-19 death MESHD among (i) public sector 'active patients' (at least 1 health visit in the 3 years before March 2020), (ii) laboratory-diagnosed COVID-19 cases and (iii) hospitalized COVID-19 cases. COVID-19 was diagnosed with SARS-CoV-2 PCR tests. We calculated the standardized mortality ratio (SMR) for COVID-19 comparing HIV positive vs. negative adults TRANS using modelled population estimates. Results: Among 3,460,932 public sector patients (16% HIV positive), 22,308 were diagnosed with COVID-19, of whom 625 died. In adjusted analysis, HIV increased risk of COVID-19 mortality (adjusted hazard ratio [aHR]:2.14; 95% confidence interval [CI]:1.70; 2.70), with similar risks across strata of viral load and immunosuppression. increased HIV-associated risk of COVID-19 death remained when restricting to COVID-19 cases (aHR:1.70; 95%CI:132; 2.18) or hospitalized cases (aHR:1.45; 95%CI:1.14; 1.84). Current and previous tuberculosis MESHD also increased COVID-19 mortality risk (aHR [95%CI]:2.70 [1.81; 4.04] and 1.51 [1.18; 1.93] respectively). The SMR for COVID-19 death MESHD associated with HIV was 2.39 (95% CI:1.96; 2.86); population attributable fraction 8.5% (95%CI:6.1; 11.1). Conclusion: HIV was associated with a doubling of COVID-19 mortality risk. While our findings may over-estimate the HIV-associated risk COVID-19 death MESHD due to residual confounding, people with HIV MESHD should be considered a high-risk group for COVID-19 management.

    COVID-19 and HIV co-infection MESHD: a living systematic evidence map of current research

    Authors: Gwinyai Masukume; Witness Mapanga; Doreen Sindisiwe van Zyl

    doi:10.1101/2020.06.04.20122606 Date: 2020-06-07 Source: medRxiv

    Abstract The world currently faces two ongoing devastating pandemics. These are the new severe acute respiratory syndrome coronavirus 2/coronavirus disease MESHD 2019 (SARS-CoV-2/COVID-19) and the prior human immunodeficiency HP immunodeficiency MESHD virus/acquired immune deficiency syndrome ( HIV MESHD/ AIDS MESHD) pandemics. The literature regarding the confluence of these global plagues expands at pace. A systematic search of the literature considering COVID-19 and HIV co-infection MESHD was performed. After five months, from the beginning of the COVID-19 pandemic, there were at least thirty-five studies reported from thirteen countries. These ranged from individual case reports and series to cohort studies. Based on studies that could be extrapolated to the general population, co-infected MESHD individuals with suppressed HIV viral loads did not have disproportionate COVID-19 sickness and death MESHD. At least four patients, newly diagnosed with HIV MESHD recovered from COVID-19. Current evidence suggests that co-infected MESHD patients should be treated like the general population. This ongoing living systematic evidence map of contemporary primary SARS-CoV-2 and HIV co-infection MESHD research provides a platform for researchers, policy makers, clinicians and others to more quickly discover and build relevant insights.

    Fatal Central Nervous System Co-Infection MESHD with SARS-CoV-2 and Tuberculosis MESHD in a Healthy Child TRANS

    Authors: Bishara J. Freij; Bassam M. Gebara; Rabail Tariq; Ay-Ming Wang; John Gibson; Nidal El-Wiher; Graham Krasan; Paul M. Patek; Kelly A. Levasseur; Mitual Amin; Joseph M. Fullmer

    doi:10.21203/rs.3.rs-33272/v1 Date: 2020-06-04 Source: ResearchSquare

    Background. Central and peripheral nervous system symptoms MESHD and complications are being increasingly recognized among individuals with pandemic SARS-CoV-2 infections MESHD, but actual detection of the virus or its RNA in the central nervous system has rarely been sought or demonstrated. Severe or fatal illnesses are attributed to SARS-CoV-2, generally without attempting to evaluate for alternative causes or co-pathogens.Case presentation. A five-year-old girl with fever HP fever MESHD and headache HP headache MESHD was diagnosed with acute SARS-CoV-2-associated meningoencephalitis MESHD based on the detection of its RNA on a nasopharyngeal swab, cerebrospinal fluid analysis, and magnetic resonance imaging findings. Serial serologic tests SERO for SARS-CoV-2 IgG and IgA showed seroconversion, consistent with an acute infection MESHD. Mental status and brain imaging findings gradually worsened despite antiviral therapy and intravenous dexamethasone. Decompressive suboccipital craniectomy for brain herniation with cerebellar biopsy on day 30 of illness, shortly before death, revealed SARS-CoV-2 RNA in cerebellar tissue using the Centers for Disease Control and Prevention 2019-nCoV Real-Time Reverse Transcriptase-PCR Diagnostic Panel. On histopathology, necrotizing granulomas MESHD granulomas HP with numerous acid-fast bacilli were visualized, and Mycobacterium tuberculosis MESHD complex DNA was detected by PCR. Ventricular cerebrospinal MESHD fluid that day was negative for mycobacterial DNA. She had no known exposures to tuberculosis MESHD and no chest radiographic findings to suggest it. All 6 family members TRANS had normal chest radiographs and negative interferon-γ release assay results. The source of her tuberculous infection MESHD was not identified, and further investigations by the local health department were not possible because of the State of Michigan-mandated lockdown for control of SARS-CoV-2 spread.Conclusion. The detection of SARS-CoV-2 RNA in cerebellar tissue and the demonstration of seroconversion in IgG and IgA assays was consistent with acute SARS-CoV-2 infection of the central nervous infection MESHD. However, the cause of death MESHD was brain herniation from her rapidly progressive central nervous system tuberculosis MESHD. SARS-CoV-2 may mask or worsen occult tuberculous infection MESHD infection with severe HP or fatal consequences.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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