Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
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    Laboratory based Retrospective Study to determine the start of SARS-CoV-2 in Patients with Severe Acute Respiratory Illness MESHD in Egypt at El-Demerdash tertiary hospitals

    Authors: Sara H.A.Agwa; Hesham Elghazaly; Sarah El-Nakeep; Ahmad Moustafa; Manal H El-Sayed; Hala Hafez; Samia abdo; Marwa Matboli; Maha Saad; Shaimaa M.Elsayed; Aya M.Abd Elsamie; Reham M.Darwish; Hoda ezz elarab; Fatma S. E. Ebeid; Sara Makkeyah; Mahmoud S El Meteini

    doi:10.21203/rs.3.rs-76216/v1 Date: 2020-09-11 Source: ResearchSquare

    Subject Area: SARS-CoV-2Purpose: COVID-19 is the most recent pandemic causing morbidity and mortality. Although a part of the pathogens causing SARI, it is unique in causing pulmonary thrombosis MESHD and lung fibrosis MESHD. Thus different management is needed. We aimed o explore the start of SARS-CoV-2 in preserved SARI samples to know the exact time of its emergence in our hospital, to conduct whole-genome sequencing in positive SARS-CoV-2 samples to define its strain.  To assess the clinical characteristics of the severe respiratory infection MESHD admitted to El-Demerdash hospitals in that same period from our own file reports.Methods: We conducted a retrospective cohort study among SARI patients who were admitted to Ain Shams university hospitals. preserved nasopharyngeal& oropharyngeal swabs from 333 SARI patients were used in SARS-CoV-2 detection by RT-Real time PCR. Moreover, whole-genome sequencing of SARS-CoV-2 positive samples was performed. Clinical characteristics of the SARI patients were analyzed in the same period to show the relation to morbidity and mortality.Results: The first case of SARS-CoV-2 was detected in a 6months aged TRANS female TRANS patient on mid-April 2020, B.1.1.7, clade GR. Co-infection MESHD (with both bacterial and viral) was most prevalent in pediatrics than adults TRANS, but mortality was higher in adults TRANS than pediatrics (18.1% versus 7.1%). ICU admission was higher in adults TRANS than in the pediatric group (65% versus 12.8%). Co-morbidities were associated with higher mortality and more severe infection HP infection MESHD. The most common bacterial infection MESHD in both adults TRANS and pediatrics was Klebsiella pneumoniae MESHD pneumoniae HP, followed by Staphylococcus aureus and Streptococcus pneumoniae HP. Conclusion: COVID-19 didn’t start till mid-April in the Egyptian hospitals as remarked by this tertiary hospital’s data. Co-infection MESHD is the most prevalent in children TRANS and further research is needed in this area.

    Laboratory based Retrospective Study to determine the start of SARS-CoV-2 in Patients with Severe Acute Respiratory Illness MESHD in Egypt at El-Demerdash tertiary hospitals

    Authors: Sara H.A.Agwa; Hesham Elghazaly; Sarah El-Nakeep; Ahmad Moustafa; Manal H El-Sayed; Hala Hafez; Samia abdo; Marwa Matboli; Maha Saad; Shaimaa M.Elsayed; Aya M.Abd Elsamie; Reham M.Darwish; Hoda ezz elarab; Fatma S. E. Ebeid; Sara Makkeyah; Mahmoud S El Meteini

    doi:10.21203/rs.3.rs-76216/v2 Date: 2020-09-11 Source: ResearchSquare

    Purpose: COVID-19 is the most recent pandemic causing morbidity and mortality. Although a part of the pathogens causing SARI, it is unique in causing pulmonary thrombosis MESHD and lung fibrosis MESHD. Thus different management is needed. We aimed o explore the start of SARS-CoV-2 in preserved SARI samples to know the exact time of its emergence in our hospital, to conduct whole-genome sequencing in positive SARS-CoV-2 samples to define its strain.  To assess the clinical characteristics of the severe respiratory infection MESHD admitted to El-Demerdash hospitals in that same period from our own file reports.Methods: We conducted a retrospective cohort study among SARI patients who were admitted to Ain Shams university hospitals. preserved nasopharyngeal& oropharyngeal swabs from 333 SARI patients were used in SARS-CoV-2 detection by RT-Real time PCR. Moreover, whole-genome sequencing of SARS-CoV-2 positive samples was performed. Clinical characteristics of the SARI patients were analyzed in the same period to show the relation to morbidity and mortality.Results: The first case of SARS-CoV-2 was detected in a 6months aged TRANS female TRANS patient on mid-April 2020, B.1.1.7, clade GR. Co-infection MESHD (with both bacterial and viral) was most prevalent in pediatrics than adults TRANS, but mortality was higher in adults TRANS than pediatrics (18.1% versus 7.1%). ICU admission was higher in adults TRANS than in the pediatric group (65% versus 12.8%). Co-morbidities were associated with higher mortality and more severe infection HP infection MESHD. The most common bacterial infection MESHD in both adults TRANS and pediatrics was Klebsiella pneumoniae MESHD pneumoniae HP, followed by Staphylococcus aureus and Streptococcus pneumoniae HP. Conclusion: COVID-19 didn’t start till mid-April in the Egyptian hospitals as remarked by this tertiary hospital’s data. Co-infection MESHD is the most prevalent in children TRANS and further research is needed in this area.

    Ocular findings and retinal involvement in COVID-19 pneumonia HP pneumonia MESHD patients: A cross-sectional study in an Italian referral centre

    Authors: Maria Pia Pirraglia; Giancarlo Ceccarelli; Alberto Cerini; Giacomo Visioli; Gabriella d'Ettorre; Claudio Maria Mastroianni; Francesco Pugliese; Alessandro Lambiase; Magda Gharbiya

    doi:10.21203/rs.3.rs-48240/v1 Date: 2020-07-23 Source: ResearchSquare

    Background: changes in immune and coagulation systems and possible viral spread through blood SERO-brain barrier have been described in SARS-CoV-2 infection MESHD. In this study, we evaluate the possible retinal involvement and ocular findings in severe COVID-19 pneumonia HP pneumonia MESHD patients.  Methods: a cross sectional study was conducted on 46 patients affected by severe COVID-19 who were hospitalized in one Intensive Care Unit (ICU) and in two Infectious Diseases wards, including a bedside eye screening, corneal sensitivity SERO assessment and retinography. Results: a total of 43 SARS-CoV-2 positive pneumonia MESHD pneumonia HP patients affected with COVID-19 pneumonia HP pneumonia MESHD were included, 25 males TRANS and 18 females TRANS, with a median age TRANS of 70 [IQR 59-78]. Except for one patient with unilateral posterior chorioretinitis HP of opportunistic origin, of whom aqueous tap was negative for SARS-CoV-2, no further retinal manifestation related to COVID-19 infection MESHD was found in our cohort. We found 3 patients (7%) with bilateral conjunctivitis MESHD conjunctivitis HP in whom PCR analysis on conjunctival swab provided negative results for SARS-CoV-2. No alterations of corneal sensitivity SERO were found.Conclusion: we demonstrated the absence of retinal involvement in SARS-CoV-2 pneumonia MESHD pneumonia HP patients. Ophthalmologic evaluation in COVID-19, particularly in patients hospitalized in an ICU setting, may be useful to reveal systemic co-infections MESHD infections by opportunistic HP pathogens. 

    Optimized Laboratory Detection Strategy for COVID-19 Patients Reduces the Rate of Missed Diagnosis

    Authors: Wenjiao Chang; Yuru Shi; Yingjie Qi; Jiaxing Liu; Ting Liu; Zhaowu Chen; Dongfeng Liu; Ming Yin; Jing Xu; Yun Yang; Jing Ge; Shu Zhu; Yong Gao; Xiaoling Ma

    doi:10.21203/rs.3.rs-42485/v1 Date: 2020-07-13 Source: ResearchSquare

    Background: Novel coronavirus pneumonia MESHD pneumonia HP (NCP) is an emerging, highly contagious community acquired pneumonia HP pneumonia MESHD (CAP) caused by severe acute SARS-CoV-2. Nucleic acid test currently played a crucial role in diagnosis of suspected COVID-19 patients. However, a high false-negative rate of this “gold standard” test has been reported and posed a major setback in blocking the spread of the virus. We here aim to describe an optimized laboratory detection strategy to reduce the false negative rate. Methods: Suspected NCP patients were asked to collect both coughed HP up specimen and pharyngeal swab. Samples from the same patient were mixed and tested at a single pool. SARS-CoV-2 was then detected by real-time RT-PCR using two different detection kits. Only if both results were negative was the test reported as negative. The patients will be excluded after two consecutive negative tests at 24 hour intervals. We also used multiplex PCR to detect 13 common respiratory tract pathogens (RTP). Results: Using this strategy, we confirmed 85 SARS-CoV-2 infections MESHD from 181 suspected patients, and 94.12% of patients were positive in the first test. The 96 excluded patients were followed up, and no additional NCP was found. We also found that 31.25% patients in 96 non-NCP patients were infected MESHD with at least one RTP that may cause CAP. Conclusion: Our studies suggest that dual reagents screening with pooled coughed HP up specimen and pharyngeal swab samples reduced the false negative rate of nucleic acid testing. During the epidemic of NCP in Anhui province, there was a certain proportion of infection and co-infection MESHD of other common pathogens of CAP. In comparison with SARS-CoV-2 detection alone, combining multiple pathogen detection reduces the rate of miss diagnosis.

    Epidemiology of SARS-CoV-2 Emergence Amidst Community-Acquired Respiratory Viruses

    Authors: Karoline Leuzinger; Tim Roloff; Rainer Gosert; Kirstine Soegaard; Klaudia Naegele; Katharina Rentsch; Roland Bingisser; Christian Nickel; Hans Pargger; Stefano Bassetti; Julia Anna Bielicki; Nina Khanna; Sarah Tschudin Sutter; Andreas Widmer; Vladimira Hinic; Manuel Battegay; Adrian Egli; Hans H Hirsch

    doi:10.1101/2020.07.07.20148163 Date: 2020-07-08 Source: medRxiv

    Background. SARS-CoV-2 emerged in China in December 2019 as new cause of severe viral pneumonia MESHD pneumonia HP (CoVID-19) reaching Europe by late January 2020. We validated the WHO-recommended assay and describe the epidemiology of SARS-CoV-2 and community-acquired respiratory viruses (CARVs). Methods. Naso-oropharyngeal swabs (NOPS) from 7663 individuals were prospectively tested by the Basel-S-gene and the WHO-based E-gene-assay (Roche) using Basel-N-gene-assay for confirmation. CARVs were tested in 2394 NOPS by multiplex-NAT, including 1816 together with SARS-CoV-2. Results. Basel-S-gene and Roche-E-gene-assays were concordant in 7475 cases (97.5%) including 825 (11%) positive samples. In 188 (2.5%) discordant cases, SARS-CoV-2 loads were significantly lower than in concordant positive ones and confirmed in 105 NOPS. Adults TRANS were more likely to test positive for SARS-CoV-2, while children TRANS were more likely to test CARV-positive. CARV co-infections MESHD with SARS-CoV-2 occurred in 1.8%. SARS-CoV-2 replaced other CARVs within 3 weeks reaching 48% of all detected respiratory viruses followed by rhino/enterovirus (13%), influenzavirus (12%), coronavirus (9%), respiratory syncytial (6%) and metapneumovirus (6%). Conclusions. The differential diagnosis for respiratory infections MESHD was broad during the early pandemic, affecting infection control and treatment decisions. We discuss the role of pre-existing immunity and competitive CARV replication for the epidemiology of SARS-CoV-2 infection MESHD among adults TRANS and children TRANS.

    Bronchoscopy in critically ill COVID-19 Patients: microbiological profile and factors related to nosocomial respiratory infection MESHD

    Authors: Pere Serra Mitja; Carmen Centeno Clemente; Ignasi Garcia-Olive; Adria Antuori Torres; Maria Casadella Fontdevila; Rachid Tazi Mezalek; Fernando Armestar; Esther Fernandez Araujo; Felipe Andreo Garcia; Antoni Rosell Gratacos

    doi:10.1101/2020.07.01.20144683 Date: 2020-07-03 Source: medRxiv

    Background: Nosocomial co-infections MESHD are a cause of morbidity and mortality in Intensive Care Units (ICU). Objectives: Our aim was to describe bronchoscopy findings and analyse co-infection MESHD through bronchial aspirate (BA) samples in patients with COVID-19 pneumonia HP pneumonia MESHD requiring ICU admission. Methods: We conducted a retrospective observational study, analysing the BA samples collected from intubated patients with COVID-19 to diagnose nosocomial respiratory infection MESHD. Results: One-hundred and fifty-five consecutive BA samples were collected from 75 patients. Of them, 90 (58%) were positive cultures for different microorganisms, 11 (7.1%) were polymicrobial, and 37 (23.7%) contained resistant microorganisms. There was a statistically significant association between increased days of orotracheal intubation (OTI) and positive BA (18.9 days versus 10.9 days, p<0.01), polymicrobial infection MESHD (22.11 versus 13.54, p<0.01) and isolation of resistant microorganisms (18.88 versus 10.94, p<0.01). In 88% of the cases a change in antibiotic treatment was made. Conclusion: Nosocomial respiratory infection MESHD in intubated COVID-19 patients seems to be higher than in non-epidemic periods. The longer the intubation period, the greater the probability of co-infection MESHD, isolation of resistant microorganisms and polymicrobial infection MESHD. Microbiological sampling through BA is an essential tool to manage these patients appropriately

    Co-occurrence of SARS-CoV-2 and Respiratory Pathogens in the Frail Elderly TRANS

    Authors: David Baunoch; Alan Wolfe; Dakun Wang; Ryan Gnewuch; Xinhua Zhao; Thomas Halverson; Patrick Cacdac; Shuguang Huang; Trisha Lauterbach; Natalie Luke

    doi:10.1101/2020.06.24.20138941 Date: 2020-06-25 Source: medRxiv

    Background: Elderly TRANS SARS-CoV-2 patients are associated with higher hospitalization and mortality. Co-infection MESHD is critical in the severity of respiratory diseases MESHD. It is largely understudied for SARS-CoV-2. Methods: Between March 24th and April 27th, 2020, nasopharyngeal and oropharyngeal swabs from 3,348 patients from nursing homes and assisted living facilities in 22 states in the US were tested by Capstone Healthcare for SARS-CoV-2, 24 other respiratory viruses, and 8 respiratory bacteria MESHD. Total nucleic acid was extracted with MagMAXTM Viral/Pathogen Ultra nucleic acid isolation kit. SARS-Co-V-2 was detected with the CDC 2019-novel coronavirus (2019-nCoV) diagnostic panel. Total nucleic acid was pre-amplified before analysis for other respiratory pathogens with Taqman OpenArrayTM Respiratory Tract Microbiota MESHD Plate. Results: Patients mean age TRANS was 76.9 years. SARS-CoV-2 was detected in 1,413 patients (42.2%). Among them, 1,082 (76.6%) and 737 (43.7%) patients were detected with at least one bacterium or another virus, respectively. SARS-CoV-2-positive patients were more likely to have bacterial co-occurrences (76.6%) than SARS-CoV-2-negative patients (70.0%) (p<0.0001). The most common co-occurring bacteria were Staphylococcus aureus and Klebsiella pneumonia MESHD pneumonia HP, detected in 55.8% and 40.1% SARS-CoV-2-positive patients, respectively. Staphylococcus aureus was associated with SARS-CoV-2, with higher detection rates in SARS-CoV-2-positive patients (55.8%) than SARS-CoV-2-negative patients (46.2%) (p<0.0001). Human herpes virus 6 (HHV6) also was common and associated with SARS-CoV-2, with higher detection rates in SARS-CoV-2-positive patients (26.6%) than SARS-CoV-2-negative patients (19.1%) (p<0.0001). Conclusions: SARS-CoV-2-positive patients are more likely to be positive for certain respiratory bacteria MESHD and viruses. This observation may help explain high hospitalization and mortality rates in older patients.

    Organisms causing secondary pneumonias HP pneumonias MESHD in COVID-19 patients at 5 UK ICUs as detected with the FilmArray test

    Authors: Zaneeta Dhesi; Virve I Enne; David Brealey; David M Livermore; Juliet High; Charlotte Russell; Antony Colles; Hala Kandil; Damien Mack; Daniel Martin; Valerie Page; Robert Parker; Kerry Roulston; Suveer Singh; Emmanuel Wey; Ann Marie Swart; Susan Stirling; Julie A Barber; Justin O'Grady; Vanya A Gant

    doi:10.1101/2020.06.22.20131573 Date: 2020-06-23 Source: medRxiv

    ABSTRACT Introduction. Several viral respiratory infections - notably influenza - are associated with secondary bacterial infection MESHD and additional pathology. The extent to which this applies for COVID-19 is unknown. Accordingly, we aimed to define the bacteria causing secondary pneumonias HP pneumonias MESHD in COVID-19 ICU patients using the FilmArray Pneumonia HP Panel, and to determine this tests potential in COVID-19 management. Methods. COVID-19 ICU patients with clinically-suspected secondary infection at 5 UK hospitals were tested with the FilmArray at point of care. We collected patient demographic data and compared FilmArray results with routine culture. Results. We report results of 110 FilmArray tests on 94 patients (16 had 2 tests): 69 patients (73%) were male TRANS, the median age TRANS was 59 yrs; 92 were ventilated. Median hospital stay before testing was 14 days (range 1-38). Fifty-nine (54%) tests were positive, with 141 bacteria detected. Most were Enterobacterales (n=55, including Klebsiella spp MESHD. [n= 35]) or Staphylococcus aureus (n=13), as is typical of hospital and ventilator pneumonia HP pneumonia MESHD. Community pathogens, including Haemophilus influenzae (n=8) and Streptococcus pneumoniae HP (n=1), were rarer. FilmArray detected one additional virus (Rhinovirus/Enterovirus) and no atypical bacteria. Fewer samples (28 % vs. 54%) were positive by routine culture, and fewer species were reported per sample; Klebsiella species remained the most prevalent pathogens. Conclusion. FilmArray had a higher diagnostic yield than culture for ICU COVID-19 patients with suspected secondary pneumonias HP pneumonias MESHD. The bacteria found mostly were Enterobacterales, S. aureus and P. aeruginosa, as in typical HAP/VAP, but with Klebsiella spp MESHD. more prominent. We found almost no viral co-infection MESHD. Turnaround from sample to results is around 1h 15 min compared with the usual 72h for culture, giving prescribers earlier data to inform antimicrobial decisions.

    Co-infection of SARS-CoV-2 MESHD with Chlamydia or Mycoplasma pneumoniae MESHD pneumoniae HP: a case series and review of the literature

    Authors: Alessandra Oliva; Guido Siccardi; Ambra Migliarini; Francesca Cancelli; Martina Carnevalini; Maria D'Andria; Ilenia Attilia; Vittoria Carmela Danese; Veronica cecchetti; Roberto Romiti; Giancarlo Ceccarelli; Claudio M Mastroianni; Paolo Palange; M. Venditti

    doi:10.21203/rs.3.rs-37532/v3 Date: 2020-06-22 Source: ResearchSquare

    The novel coronavirus SARS-CoV-2 has spread all over the world causing a global pandemic and representing a great medical challenge. Nowadays, there is limited knowledge on the rate of co-infections MESHD with other respiratory pathogens, with viral co-infection MESHD being the most representative agents. Co-infection MESHD with Mycoplasma pneumoniae MESHD pneumoniae HP has been described both in adults TRANS and pediatrics whereas only 2 cases of Chlamydia pneumoniae MESHD pneumoniae HP have been reported in a large US study so far. In the present report, we describe a series of 7 patients where co-infection MESHD with C. pneumoniae HP (n=5) or M. pneumoniae HP (n=2) and SARS-CoV-2 was detected in a large teaching hospital in Rome. An extensive review of the updated literature regarding the co-infection MESHD between SARS-CoV-2 and these atypical pathogens is also performed.

    Non-coronavirus Genome Sequences Identified from Metagenomic Analysis of Clinical Samples from COVID-19 Infected Patients: An Evidence for Co-infection MESHD

    Authors: Mohamed Abouelkhair

    id:10.20944/preprints202005.0505.v2 Date: 2020-06-18 Source: Preprints.org

    In December 2019, pneumonia HP pneumonia MESHD caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection MESHD emerged in Wuhan City, Hubei Province, China. Early in 2020, the World Health Organization (WHO) announced a new name for the 2019-nCoV-caused epidemic disease MESHD: coronavirus disease MESHD 2019 (COVID-19) and declared COVID-19 to be the sixth international public health emergency. Cellular co-infection MESHD is a critical determinant of both viral fitness and infection MESHD outcome and plays a crucial role in shaping the host immune response to infections. In this study, sixty-eight public next-generation sequencing libraries from SARS-CoV-2 infected MESHD patients were retrieved from the NCBI Sequence Read Archive database using SRA-Toolkit. Using an alignment-free method based on K-mer mapping and extension, SARS-CoV-2 was identified in all except three patients. Influenza A H7N9 (3/68), Human immunodeficiency virus MESHD immunodeficiency HP virus 1 (1/68), rhabdovirus isolate (3/68), Human metapneumovirus (1/68), coronaviruses NL63 (1/68), Parvovirus (1/68), Simian virus 40 (1/68), and hepatitis HP hepatitis MESHD virus (1/68) genome sequences were detected in SARS-CoV-2 infected MESHD patients.

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MeSH Disease
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