Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
    displaying 21 - 30 records in total 75
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    COVID-19 among people living with HIV MESHD: A systematic review

    Authors: Hossein Mirzaei; Willi McFarland; Mohammad Karamouzian; Hamid Sharifi

    doi:10.1101/2020.07.11.20151688 Date: 2020-07-14 Source: medRxiv

    This systematic review summarizes the evidence on the earliest patients with COVID-19-HIV co-infection MESHD. We searched PubMed, Scopus, Web of Science, Embase, preprint databases, and Google Scholar from December 01, 2019 to June 1, 2020. From an initial 547 publications and 75 reports, 25 studies provided specific information on COVID-19 patients living with HIV MESHD. Studies described 252 patients, 80.9% were male TRANS, mean age TRANS was 52.7 years, and 98% were on ART. Co-morbidities in addition to HIV and COVID-19 (multimorbidity) included hypertension HP hypertension MESHD (39.3%), obesity HP obesity MESHD or hyperlipidemia HP (19.3%), chronic obstructive pulmonary disease HP chronic obstructive pulmonary disease MESHD (18.0%), and diabetes MESHD (17.2%). Two-thirds (66.5%) had mild to moderate symptoms, the most common being fever HP fever MESHD (74.0%) and cough HP (58.3%). Among patients who died, the majority (90.5%) were over 50 years old, male TRANS (85.7%), and had multimorbidity (64.3%). Our findings highlight the importance of identifying co-infections MESHD, addressing co-morbidities, and ensuring a secure supply of ART for PLHIV during the COVID-19 pandemic.

    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.

    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.

    A preceding low-virulence strain pandemic inducing immunity against COVID-19

    Authors: Hagai Perets; Ruth Perets

    doi:10.21203/rs.3.rs-41098/v1 Date: 2020-07-11 Source: ResearchSquare

    The COVID-19 pandemic is thought to began in Wuhan, China in December 2019. Mobility analysis identified East-Asia and Oceania countries to be highly-exposed to COVID-19 spread, consistent with the earliest spread occurring in these regions. However, here we show that while a strong positive correlation between case-numbers and exposure level could be seen early-on as expected, at later times the infection-level is found to be negatively correlated with exposure-level. Moreover, the infection MESHD level is positively correlated with the population size, which is puzzling since it has not reached the level necessary for population-size to affect infection-level through herd immunity. These issues are resolved if a low-virulence Corona-strain (LVS) began spreading earlier in China outside of Wuhan, and later globally, providing immunity from the later appearing high-virulence strain (HVS). Following its spread into Wuhan, cumulative mutations gave rise to the emergence of an HVS, known as SARS-CoV-2, starting the COVID-19 pandemic. We model the co-infection MESHD by an LVS and an HVS and show that it can explain the evolution of the COVID-19 pandemic and the non-trivial dependence on the exposure level to China and the population-size in each country. We find that the LVS began its spread a few months before the onset of the HVS MESHD and that its spread doubling-time is \sim1.59\pm0.17 times slower than the HVS. Although more slowly spreading, its earlier onset allowed the LVS to spread globally before the emergence of the HVS. In particular, in countries exposed earlier to the LVS and/or having smaller population-size, the LVS could achieve herd-immunity earlier, and quench the later-spread HVS at earlier stages. We find our two-parameter (the spread-rate and the initial onset time of the LVS) can accurately explain the current infection levels (R^2=0.74); p-value (p) of 5.2x10^-13). Furthermore, countries exposed early should have already achieved herd-immunity. We predict that in those countries cumulative infection levels could rise by no more than 2-3 times the current level through local-outbreaks, even in the absence of any containment measures. We suggest several tests and predictions to further verify the double-strain co-infection MESHD model and discuss the implications of identifying the LVS.

    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.

    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.

    Profiling pre-symptomatic and asymptomatic TRANS cases with confirmed TRANS SARS-CoV-2 infection MESHD in Mexico City

    Authors: Omar Yaxmehen Bello-Chavolla; Neftali Eduardo Antonio-Villa; Arsenio Vargas-Vázquez; Carlos A. Fermín-Martínez; Alejandro Márquez-Salinas; Jessica Paola Bahena-López

    doi:10.1101/2020.07.02.20145516 Date: 2020-07-04 Source: medRxiv

    BACKGROUND: Asymptomatic TRANS SARS-CoV-2 infections MESHD are potential sources for transmission TRANS. OBJECTIVES: Here, we aimed to profile pre-symptomatic/ asymptomatic TRANS SARS-CoV-2 infections MESHD in Mexico City, its associated comorbidities and outcomes. METHODS: Prospective observational study of SARS-CoV-2 cases assessed by contact tracing TRANS within the National Epidemiological Surveillance System in Mexico City. We classified subjects as cases with and without respiratory and non-respiratory symptoms ( RS MESHD, NRS, respectively) assessed for SARS-CoV-2 using real time RT-PCR from nasopharyngeal swabs to evaluate clinical characteristics as well as features associated with severe COVID-19. RESULTS: Amongst 80735 cases with confirmed TRANS SARS-CoV-2 infection MESHD as of July 23th, 2020, we identified 9659 cases without RS MESHD (12.0%), 5605 had only NRS (6.9%) and 4054 who were initially asymptomatic TRANS (5.1%). Compared to asymptomatic TRANS cases, those with NRS and those with RS MESHD+NRS had higher rates of severe COVID-19 outcomes including hospitalization, ICU admission, and intubation (p<0.001). Mortality was higher for cases with RS MESHD+NRS (HR 7.58, 95%CI 4.56-12.58) or NRS (HR 3.13, 95%CI 1.80-5.45) compared to asymptomatic TRANS cases, adjusted for age TRANS, sex and comorbidities. Predictors for mortality in asymptomatic TRANS SARS-Co-V-2 infections MESHD infections, chronic HP chronic kidney disease MESHD, previous exposure with suspected infection MESHD cases and older age TRANS were predictors for lethality. CONCLUSIONS: Definition of pre-symptomatic/ asymptomatic TRANS cases has relevant implications for SARS-CoV-2 infection MESHD outcomes. Older age TRANS and comorbidity impact on the probability of developing severe complications for cases who were asymptomatic TRANS or had only NRS at evaluation and were sent for domiciliary treatment. Extending testing for detection of asymptomatic TRANS cases must be considered in Mexico to better understand the impact of the pandemic.

    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

    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.

    Influence of influenza A virus in COVID-19 patients: A retrospective cohort study

    Authors: Yuan Cheng; Jing Ma; He Wang; Xi Wang; Zhanwei Hu; Haichao Li; Hong Zhang; Xinmin Liu

    doi:10.21203/rs.3.rs-39932/v1 Date: 2020-07-02 Source: ResearchSquare

    Background and objective: Coronavirus disease (COVID-19) is currently an urgent global issue, but we cannot ignore the impact of influenza A since there is an overlap of infection time and region and similar clinical manifestations and chest computed tomography (CT) images for influenza A and COVID-19 infections. We compared patients who had a COVID-19 infection MESHD and co-infection MESHD with the influenza A virus.Methods: We retrospectively reviewed patients who met the inclusion criteria for this study.Results: There were 213 patients included in this study, of whom 106 were females TRANS and 107 were males TRANS, with a median age TRANS of 63 years. All patients were diagnosed with COVID-19 and were subsequently divided into influenza positive (n = 97) and influenza negative (n = 116) groups according to the serum SERO test results for the influenza A IgM antibody SERO. The two groups had similar symptoms, outcomes, CT manifestation and CT scores, except for lymphadenopathy HP lymphadenopathy MESHD (6.2% in the influenza positive group vs. 14.7% in the negative group, P = 0.047). However, in the subgroup analysis, male TRANS or younger patients ( age TRANS <= 60 years) in the influenza negative group had higher CT scores than patients in the influenza positive group (P < 0.05).Conclusions: COVID-19 patients who had co-infection MESHD with the influenza A virus showed similar symptoms, outcomes, CT manifestation and CT scores to influenza negative patients. However, male TRANS patients and younger patients had higher CT scores in the influenza negative group.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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