Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (304)

Fever (167)

Cough (107)

Hypertension (91)

Respiratory distress (91)


Transmission

age categories (586)

Transmission (495)

asymptotic cases (252)

gender (244)

fomite (192)


Seroprevalence
    displaying 1331 - 1340 records in total 2851
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    Early administration of lopinavir/ritonavir plus hydroxychloroquine does not alter the clinical course of SARS-CoV-2 infection MESHD: a retrospective cohort study.

    Authors: Andrea Giacomelli; Gabriele Pagani; Anna Lisa Ridolfo; Alice Oreni; Federico Conti; Laura Pezzati; Lucia Bradanini; Giacomo Casalini; Simone Passerini; Alessandro Torre; Massimo Cohen; Guido Gubertini; Giuliano Rizzardini; Chiara Cogliati; Elisa Ceriani; Riccardo Colombo; Stefano Rusconi; Cristina Gervasoni; Dario Cattaneo; Spinello Antinori; Massimo Galli

    doi:10.1101/2020.06.05.20123299 Date: 2020-06-12 Source: medRxiv

    Background The potential benefit of a combination therapy with lopinavir/ritonavir (LPV/r) and hydroxychloroquine (HCQ) on COVID-19 has been speculated. We explored the effect of the timing of LPV/r + HCQ initiation on the outcome of patients with COVID-19. Methods A retrospective cohort study was conducted on patients with COVID-19 who started treatment with LPV/r plus HCQ between February 21 and March 20, 2020, at Luigi Sacco Hospital in Milan, Italy. Over time cumulative incidence of clinical improvement was compared between patients who started treatment less than 5 days from the onset of symptoms TRANS [early treatment group (ET)] and those who initiated it later [delayed treatment group (DT)]. The association of LPV/r plus HCQ initiation timing on 30-day mortality was also assessed by univariate and multivariate logistic models. Results The study included 172 patients, prevalently males TRANS (72%) in their sixties, with a moderate (53.4%) or severe (34.9%) disease. Fourty-three (25%) patients were included in the ET group and and 129 (75%) in the DT group. Severity of disease did not significantly differ between the two groups. Conclusion Timing of LPV/r + HCQ initiation seems to have no impact on COVID-19 clinical course in terms of improvement and 30-day mortality. These findings rise doubts on the clincial efficacy of this regimen.

    Asymptomatic TRANS carriage rates and case-fatality of SARS-CoV-2 infection MESHD in residents and staff in Irish nursing homes

    Authors: Sean P Kennelly; Adam H Dyer; Ruth Martin; Siobhan M Kennelly; Alan Martin; Desmond O'Neill; Aoife Fallon

    doi:10.1101/2020.06.11.20128199 Date: 2020-06-12 Source: medRxiv

    Background: SARS-CoV-2 has disproportionately affected nursing home (NH) residents. In Ireland, the first NH case of COVID-19 occurred on 16/03/2020. A national point- prevalence SERO testing program of all NH residents and staff took place from 18/04/2020-05/05/2020. Aims: To examine characteristics of NHs across three Community Health Organisations (CHOs) in Ireland, proportions with COVID-19 outbreaks, staff and resident, symptom-profile and resident case-fatality. Methods: Forty-five NHs surveyed across three CHOs requesting details on occupancy, size, COVID-19 outbreak, timing of outbreak, total symptomatic/ asymptomatic TRANS cases, and outcomes for residents from 29/02/2020-22/05/2020. Results: Surveys were returned from (62.2%, 28/45) of NHs (2043 residents, 2303 beds). Three-quarters (21/28) had COVID-19 outbreaks (1741 residents, 1972 beds). Median time from first case of COVID-19 in Ireland to first case in these NHs was 27.0 days. Resident COVID-19 incidence was (43.9%, 764/1741): laboratory-confirmed (40.1%, 710/1741) with (27.2%, 193/710 asymptomatic TRANS), and clinically-suspected (3.1%, 54/1741). Resident case-fatality was (27.6%, 211/764) for combined laboratory-confirmed/clinically-suspected COVID-19. Similar proportions of residents in NH with an early outbreak (<28days) versus a later outbreak developed confirmed/suspected COVID-19. A lower proportion of residents in NHs with early outbreaks had recovered compared to those with late outbreaks (37.4% vs 61.7%; X2=56.9, p<0.001). Among 675 NH staff across twenty-four sites who had confirmed/suspected COVID-19 (23.6%, 159/675) were asymptomatic TRANS. There was a significant correlation between the proportion of staff with symptomatic COVID-19 and resident numbers with confirmed/suspected COVID-19 (Spearmans rho=0.81, p<0.001). Conclusion: This study demonstrates COVID-19 impact on NH residents and staff. High infection rates lead to challenges in care provision.

    Serology-informed estimates of SARS-COV-2 infection MESHD fatality risk in Geneva, Switzerland

    Authors: Javier Perez-Saez; Stephen A Lauer; Laurent Kaiser; Simon Regard; Elisabeth Delaporte; Idris Guessous; Silvia Stringhini; Andrew S Azman; - Serocov-POP Study Group

    doi:10.1101/2020.06.10.20127423 Date: 2020-06-12 Source: medRxiv

    The infection fatality risk (IFR) is the average number of deaths per infection MESHD by a pathogen and is key to characterizing the severity of infection MESHD across the population and for specific demographic groups. To date, there are few empirical estimates of IFR published due to challenges in measuring infection rates. Outside of closed, closely surveilled populations where infection MESHD rates can be monitored through viral surveillance, we must rely on indirect measures of infection MESHD, like specific antibodies SERO. Representative seroprevalence SERO studies provide an important avenue for estimating the number of infections MESHD in a community, and when combined with death counts can lead to robust estimates of the IFR. We estimated overall and age TRANS-specific IFR for the canton of Geneva, Switzerland using age TRANS-stratified daily case and death MESHD incidence reports combined with five weekly population-based seroprevalence SERO estimates. From February 24th to June 2nd there were 5'039 confirmed cases TRANS and 286 reported deaths within Geneva (population of 506'765). We inferred age TRANS-stratified (5-9, 10-19, 20-49, 50-65 and 65+) IFRs by linking the observed number of deaths MESHD to the estimated number of infected individuals from each serosurvey. We account for the delays between infection MESHD and seroconversion as well as between infection MESHD and death MESHD. Inference is drawn in a Bayesian framework that incorporates uncertainty in seroprevalence SERO estimates (supplement). Of the 286 reported deaths MESHD caused by SARS-CoV-2, the youngest person to die was 31 years old. Infected individuals younger than 50 years experienced statistically similar IFRs (range 0.00032-0.0016%), which increases to 0.14% (95% CrI 0.096-0.19) for those 50-64 years old to 5.6% (95% CrI 4.3-7.4) for those 65 years and older (supplement). After accounting for demography and age TRANS-specific seroprevalence SERO, we estimate a population-wide IFR of 0.64% (95% CrI 0.38-0.98). Our results are subject to two notable limitations. Among the 65+ age group TRANS that died of COVID-19 within Geneva, 50% were reported among residents of assisted care facilities, where around 0.8% of the Geneva population resides. While the serosurvey protocol did not explicitly exclude these individuals, they are likely to have been under-represented. This would lead to an overestimation of the IFR in the 65+ age group TRANS if seroprevalence SERO in this institutionalized population was higher than in the general population (supplement). Further, our IFR estimates are based on current evidence regarding post-infection antibody SERO kinetics, which may differ between severe and mild infections MESHD. If mild infections MESHD have significantly lower and short-lived antibody SERO responses, our estimates of IFR may be biased upwards. Estimates of IFR are key for understanding the true pandemic burden and for weighing different risk reduction strategies. The IFR is not solely determined by host and pathogen biology, but also by the capacity of health systems to treat severe cases. Despite having among the highest per capita incidence in Switzerland, Geneva's health system accommodated the influx of cases needing intensive care (peak of 80/110 ICU-beds including surge capacity) while maintaining care quality standards. As such, our IFR estimates can be seen as a best-case scenario with respect to health system capacity. Our results reveal that population-wide estimates of IFR mask great heterogeneity by age TRANS and point towards the importance of age TRANS-targeted interventions to reduce exposures among those at highest risk of death MESHD.

    Persistent SARS-CoV-2 replication in severe COVID-19

    Authors: Maria Dolores Folgueira; Joanna Luczkowiak; Fatima Lasala; Alfredo Perez-Rivilla; Rafael Delgado

    doi:10.1101/2020.06.10.20127837 Date: 2020-06-12 Source: medRxiv

    Background: The diagnosis of SARS-CoV-2 infection MESHD is based on viral RNA detection by real-time RT-PCR (rRT-PCR) in respiratory samples. This detection can remain positive for weeks without implying virus viability. Methods: We have performed cell culture to assess viral replication in 106 respiratory samples rRT-PCR positive for SARS-CoV-2 from 105 patients with COVID-19. Fifty were samples from 50 patients with mild forms of COVID-19 who did not require hospital admission. Fifty-six samples were obtained from 55 hospitalized patients with severe pneumonia HP pneumonia MESHD. Samples were obtained at different time points covering the time from clinical diagnosis to the follow up during hospital care. Results: In 49 samples (49/106, 46.2%) a cytopathic effect (CPE) was detected in cell culture. Our study demonstrates that while in patients with mild COVID-19, viral viability is maintained in fact up to 10 days in patients with severe COVID-19 the virus can remain viable for up to 32 days after the onset of symptoms TRANS. Patients with severe COVID-19 as compared with mild cases, presented infective virus in a significantly higher proportion in samples with moderate or low viral load (Ct value > 26): 22/46 (47.8%) versus 7/38 (18.4%), (p <0.01), respectively. Conclusions: Persistent SARS-CoV-2 replication could be demonstrated in severe COVID-19 cases for periods up to 32 days after the onset of symptoms TRANS and even at high Ct values. COVID-19 severity is a more determining factor for viral viability than the time elapsed since the onset of symptoms TRANS or the Ct value obtained in the RT-PCR assay.

    Pre exposure Hydroxychloroquine use is associated with reduced COVID19 risk in healthcare workers

    Authors: Raja Bhattacharya; Sampurna Chowdhury; Rishav Mukherjee; Anita Nandi; Manish Kulshrestha; Rohini Ghosh; Souvik Saha

    doi:10.1101/2020.06.09.20116806 Date: 2020-06-12 Source: medRxiv

    Abstract Background: While several trials are ongoing for treatment of COVID-19, scientific research on chemoprophylaxis is still lacking even though it has potential to delay the pandemic allowing us time to complete research on vaccines. Methods: We have conducted a cohort study amongst Health Care Workers (HCW) exposed to COVID-19 patients, at a tertiary care center in India where there was an abrupt cluster outbreak within on duty personnel. HCWs who had voluntarily taken hydroxychloroquine (HCQ) prior to exposure were considered one cohort while those who had not were considered to be another. All participants with a verifiable contact history were tested for COVID-19 by rtPCR. The two cohorts were comparable in terms of age TRANS, gender TRANS, comorbidities and exposure. The primary outcome was incidence rates of rtPCR positive COVID-19 infection amongst HCQ users and non - users. Results: 106 healthcare workers were examined in this cohort study of whom 54 were HCQ users and rest were not. The comparative analysis of incidence of infection MESHD between the two groups demonstrated that voluntary HCQ usage was associated with lesser likelihood of developing SARS-CoV-2 infection MESHD, compared to those who were not on it, X2=14.59, p<0.001. None of the HCQ users noted any serious adverse effects. Conclusions: This study demonstrated that voluntary HCQ consumption as pre-exposure prophylaxis by HCWs is associated with a statistically significant reduction in risk of SARS-CoV-2. These promising findings therefore highlight the need to examine this association in greater detail among a larger sample using Randomised Controlled Trials (RCT).

    Interregional SARS-CoV-2 spread from a single introduction outbreak in a meat-packing plant in northeast Iowa

    Authors: Craig S Richmond; Arick P Sabin; Dean A Jobe; Steven D Lovrich; Paraic A Kenny

    doi:10.1101/2020.06.08.20125534 Date: 2020-06-12 Source: medRxiv

    SARS-CoV-2 spread has proven to be especially difficult to mitigate in high risk settings, including nursing homes, cruises, prisons and various industrial settings. Among industrial settings, meat processing facilities in the United States have experienced particularly challenging outbreaks. We have sequenced SARS-CoV-2 whole viral genomes from individuals testing positive in an integrated regional healthcare system serving 21 counties in southwestern Wisconsin, northeastern Iowa and southeastern Minnesota, providing an overview of SARS-CoV-2 introduction MESHD and spread in a region spanning multiple jurisdictions with differing mitigation policies. While most viral introductions we detected were contained with only minor transmission chains TRANS, a striking exception was an outbreak associated with a meatpacking plant in Postville, IA. In this case, a single viral introduction led to unrestrained spread within the facility, affecting many staff and members of their households. Importantly, by surveilling viral sequences from the surrounding counties, we have documented the spread of this SARS-CoV-2 substrain from this epicenter to individuals in 13 cities in 7 counties in Iowa, Wisconsin and Minnesota, a region spanning 185 square miles. This study highlights the regional public health consequences of failures to rapidly act to mitigate viral spread in a single industrial setting.

    Clinical Characteristics and Comparative Analysis of Covid-19 Patients With or Without HIV Coinfection MESHD in Wuhan, China

    Authors: Rongrong Yang; Xien Gui; Yongxi Zhang; Yong Xiong; Shicheng Gao; Hengning Ke

    doi:10.21203/rs.3.rs-34735/v1 Date: 2020-06-12 Source: ResearchSquare

    Background: COVID-19 is a public health emergency that is spreading worldwide and seriously affecting global economy. Information about the impact of HIV co-infection MESHD and anti-HIV drugs on the clinical characteristics and prognosis of COVID-19 patients remains limited.Methods: In this retrospective study, the maximum body temperatures, fever HP fever MESHD duration, chest computed tomography changes and viral shedding, lymphocyte counts changes and titer of SARS-CoV-2 antibody SERO were compared between COVID-19 patients with and without HIV infection MESHD in Zhongnan Hospital of Wuhan University from January 20th to February 14th, 2020. Results: Compared with 50 control COVID-19 patients, the two COVID-19/ HIV co-infection MESHD patients had higher maximum body temperatures(40.2℃ and 40.3℃ vs 38.2℃), longer fever HP fever MESHD duration(11 days and 15 days vs 7 days), longer time of lung recovery(20 days and 24 days vs 14 days), shorter duration of viral shedding after the onset of symptoms TRANS(6 days and 4 days vs 10 days). Compared with three COVID-19 infection MESHD colleagues who had exposure history with the same COVID-19 patient, the third COVID-19/ HIV co-infection MESHD patient had the same duration of viral shedding after exposure(29 days vs 29 days), lower titer of SARS-CoV-2 IgG MESHD(negative vs positive for all). Conclusion: For patients co-infected MESHD with HIV MESHD, the clinical manifestations of SARS-CoV-2 infection MESHD were diverse. The ability of those COVID-19/ HIV co-infection MESHD patients with severe immunodeficiency HP immunodeficiency MESHD to produce SARS-CoV-2 antibodies SERO were weakened. The small sample in this study implied that the effects of anti-HIV drugs in prevention and treatment of COVID-19 appears to be limited.

    Coronavirus and birth in Italy: results of a national population-based cohort study

    Authors: Alice Maraschini; Edoardo Corsi; Michele Antonio Salvatore; Serena Donati

    doi:10.1101/2020.06.11.20128652 Date: 2020-06-12 Source: medRxiv

    Introduction The study was implemented to provide guidance to decision makers and clinicians by describing hospital care offered to women who gave birth with confirmed COVID 19 infection MESHD. Materials and methods National population based prospective cohort study involving all women with confirmed COVID 19 who gave birth between February 25 and April 22, 2020 in any Italian hospital. Results The incidence rate of confirmed SARS-CoV-2 infection MESHD in women who gave birth was 2.1 per 1000 maternities at a national level and 6.9/1000 in the Lombardy Region. Overall one third of the women developed a pneumonia HP pneumonia MESHD and 49.7% assumed at least one drug. Caesarean section rate was 32.9%, no mothers nor newborns died. Six percent of the infants tested positive for SARS CoV 2 at birth. Conclusions Clinical features and outcomes of COVID 19 in women who gave birth are similar to those described for the general population, most women developing mild to moderate illness.

    Profiling the positive detection rate of SARS-CoV-2 using polymerase chain reaction in different types of clinical specimens: a systematic review and meta-analysis

    Authors: George M. Bwire; Mtebe V. Majigo; Belinda J. Njiro; Akili Mawazo

    doi:10.1101/2020.06.11.20128389 Date: 2020-06-12 Source: medRxiv

    Background: Testing is one of the commendable preventive measures against coronavirus disease MESHD (COVID_19), and needs to be done using both most appropriate specimen and an accurate diagnostic test like real time reverse transcription polymerase chain reaction (qRT_PCR). However, the detection rate of severe acute respiratory syndrome coronavirus 2 MESHD (SARS_CoV_2) RNA from different clinical specimens after onset of symptoms TRANS is not yet well established. For guiding the selection of specimens for clinical diagnosis of COVID-19, a systematic review aiming at profiling the positive detection rate from different clinical specimens using PCR was conducted. Methods: The systematic search was done using PubMed/MEDLINE, Science direct, Google Scholar, among others. The search included studies on laboratory diagnosis of SARS_CoV_2 from different clinical specimens using PCR. Data extraction was done using Microsoft Excel spread sheet 2010 and reported according to PRISMA_P guidelines. Using Open Meta Analyst software, DerSimonian_Laird random effects analysis was performed to determine a summary estimate (positive rate [PR]/proportions) and their 95% confidence interval (95%CI). Results: A total of 8136 different clinical specimens were analyzed to detect SARS_CoV_2, with majority being nasopharyngeal swabs (69.6%). Lower respiratory tract (LRT) specimens had a PR of 71.3% (95%CI:60.3%-82.3%) while no virus was detected from the urinogenital specimens. Bronchoalveolar lavage fluid MESHD ( BLF MESHD) specimen had the PR of 91.8% (95%CI:79.9-103.7%), followed by rectal swabs, 87.8 % (95%CI:78.6%-96.9%) then sputum, 68.1% (95%CI:56.9%-79.4%). Low PR was observed in oropharyngeal swabs, 7.6% (95%CI:5.7%-9.6%) and blood SERO samples, 1.0% (95%CI: -0.1%-2.1%), whilst no SARS-CoV-2 was detected in urine samples. Nasopharyngeal swab, a widely used specimen had a PR of 45.5% (95%CI:31.2%-59.7%). Conclusion: In this study, SARS-CoV-2 was highly detected in lower respiratory tract specimens while there was no detected virus in urinogenital specimens. Regarding the type of clinical specimens, bronchoalveolar lavage fluid had the highest positive rate followed by rectal swab then sputum. Nasopharyngeal swab which is widely used had a moderate detection rate. Low positive rate was recorded in oropharyngeal swab and blood SERO sample while no virus was found in urine samples. More importantly, the virus was detected in feces, suggesting SARS-CoV-2 transmission TRANS by the fecal route.

    Age TRANS-dependent assessment of genes involved in cellular senescence, telomere and mitochondrial pathways in human lung tissue of smokers, COPD MESHD and IPF: Associations with SARS-CoV-2 COVID-19 ACE2-TMPRSS2-Furin-DPP4 axis

    Authors: Krishna P. Maremanda; Isaac K. Sundar; Dongmei Li; Irfan Rahman

    doi:10.21203/rs.3.rs-35347/v1 Date: 2020-06-12 Source: ResearchSquare

    Aging is one of the key contributing factors for chronic obstructive pulmonary diseases HP obstructive pulmonary diseases MESHD ( COPD MESHD) and other chronic inflammatory lung diseases MESHD. Cigarette smoke is a major etiological risk factor that has been shown to alter cellular processes involving mitochondrial function, cellular senescence and telomeric length. Here we determined how aging contribute to the alteration in the gene expression of above mentioned cellular processes that play an important role in the progression of COPD MESHD and IPF. We hypothesized that aging may differentially alter the expression of mitochondrial, cellular senescence and telomere genes in smokers and patients with COPD MESHD and IPF compared to non-smokers. Total RNA from human lung tissues from non-smokers, smokers, and patients with COPD MESHD and IPF were processed and analyzed based on their ages TRANS (younger: <55 yrs and older: >55 yrs). NanoString nCounter panel was used to analyze the gene expression profiles using a custom designed codeset containing 112 genes including 6 housekeeping controls (mitochondrial biogenesis and function, cellular senescence, telomere replication and maintenance). mRNA counts were normalized, log2 transformed for differential expression analysis using linear models in the limma package (R/Bioconductor). Data from non-smokers, smokers and patients with COPD MESHD and IPF MESHD were analyzed based on the age groups TRANS (pairwise comparisons between younger vs. older groups). Several genes were differentially expressed in younger and older smokers, and patients with COPD MESHD and IPF compared to non-smokers which were part of the mitochondrial biogenesis/function (HSPD1, FEN1, COX18, COX10, UCP2 & 3), cellular senescence (PCNA, PTEN, KLOTHO, CDKN1C, TNKS2, NFATC1 & 2, GADD45A) and telomere replication/maintenance (PARP1, SIRT6, NBN, TERT, RAD17, SLX4, HAT1) target genes. Interestingly, NOX4 and TNKS2 were increased in the young IPF as compared to the young COPD MESHD patients. Genes in the mitochondrial dynamics and other quality control mechanisms like FIS1 and RHOT2 were decreased in young IPF compared to their age TRANS matched COPD subjects. ERCC1 (Excision Repair Cross-Complementation Group 1) and GADD45B were higher in young COPD as compared to IPF. Aging plays an important role in various infectious diseases MESHD. Elderly TRANS patients with chronic lung disease HP chronic lung disease MESHD and smokers were found to have high incidence and mortality rates in the current pandemic of SARS-CoV-2 infection MESHD. Immunoblot analysis in the lung homogenates of smokers, COPD MESHD and IPF subjects revealed increased protein abundance of important proteases and spike proteins like TMPRSS2, furin and DPP4 in association with a slight increase in SARS-CoV-2 receptor ACE2 levels. This may further strengthen the observation that smokers, COPD MESHD and IPF subjects are more prone to COVID-19 infection MESHD. Overall, these findings suggest that altered transcription of target genes that regulate mitochondrial function, cellular senescence, and telomere attrition add to the pathobiology of lung aging in COPD MESHD and IPF and other smoking-related chronic lung disease HP lung disease MESHD in associated with alterations in SARS-CoV-2 ACE2-TMPRSS2-Furin-DPP4 axis for COVID-19 infection MESHD.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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