Corpus overview


Overview

MeSH Disease

Human Phenotype

Hypertension (31)

Fever (31)

Cough (25)

Pneumonia (17)

Obesity (15)


Transmission

Seroprevalence
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    An improved methodology for estimating the prevalence SERO of SARS-CoV-2

    Authors: Virag Patel; Catherine McCarthy; Rachel A Taylor; Ruth Moir; Louise A Kelly; Emma L Snary

    doi:10.1101/2020.08.04.20168187 Date: 2020-08-06 Source: medRxiv

    Since the identification of Coronavirus disease MESHD 2019 (COVID-19) caused by severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) in China in December 2019, there have been more than 17 million cases of the disease MESHD in 216 countries worldwide. Comparisons of prevalence SERO estimates between different communities can inform policy decisions regarding safe travel TRANS between countries, help to assess when to implement (or remove) disease MESHD control measures and identify the risk of over-burdening healthcare providers. Estimating the true prevalence SERO can, however, be challenging because officially reported figures are likely to be significant underestimates of the true burden of COVID-19 within a community. Previous methods for estimating the prevalence SERO fail to incorporate differences between populations (such as younger populations having higher rates of asymptomatic TRANS cases) and so comparisons between, for example, countries, can be misleading. Here, we present an improved methodology for estimating COVID-19 prevalence SERO. We take the reported number of cases and deaths MESHD (together with population size) as raw prevalence SERO for the population. We then apply an age TRANS-adjustment to this which allows the age TRANS-distribution of that population to influence the case-fatality rate and the proportion of asymptomatic TRANS cases. Finally, we calculate the likely underreporting factor for the population and use this to adjust our prevalence SERO estimate further. We use our method to estimate the prevalence SERO for 166 countries (or the states of the United States of America, hereafter referred to as US state) where sufficient data were available. Our estimates show that as of the 30th July 2020, the top three countries with the highest estimated prevalence SERO are Brazil (1.26%, 95% CI: 0.96 - 1.37), Kyrgyzstan (1.10%, 95% CI: 0.82 - 1.19) and Suriname (0.58%, 95% CI: 0.44 - 0.63). Brazil is predicted to have the largest proportion of all the current global cases (30.41%, 95%CI: 27.52 - 30.84), followed by the USA (14.52%, 95%CI: 14.26 - 16.34) and India (11.23%, 95%CI: 11.11 - 11.24). Amongst the US states, the highest prevalence SERO is predicted to be in Louisiana (1.07%, 95% CI: 1.02 - 1.12), Florida (0.90%, 95% CI: 0.86 - 0.94) and Mississippi (0.77%, 95% CI: 0.74 - 0.81) whereas amongst European countries, the highest prevalence SERO is predicted to be in Montenegro (0.47%, 95% CI: 0.42 - 0.50), Kosovo (0.35%, 95% CI: 0.29 - 0.37) and Moldova (0.28%, 95% CI: 0.23 - 0.30). Our results suggest that Kyrgyzstan (0.04 tests per predicted case), Brazil (0.04 tests per predicted case) and Suriname (0.29 tests per predicted case) have the highest underreporting out of the countries in the top 25 prevalence SERO. In comparison, Israel (34.19 tests per predicted case), Bahrain (19.82 per predicted case) and Palestine (9.81 tests per predicted case) have the least underreporting. The results of this study may be used to understand the risk between different geographical areas and highlight regions where the prevalence SERO of COVID-19 is increasing most rapidly. The method described is quick and easy to implement. Prevalence SERO estimates should be updated on a regular basis to allow for rapid fluctuations in disease MESHD patterns.

    Asthma MESHD Asthma HP and COVID-19 - A systematic review

    Authors: Natália F. Mendes; Carlos P. Jara; Eli Mansour; Eliana P. Araújo; Licio Velloso

    doi:10.21203/rs.3.rs-53998/v1 Date: 2020-08-05 Source: ResearchSquare

    BackgroundSevere coronavirus disease MESHD-19 (COVID-19) presents with progressive dyspnea MESHD dyspnea HP, which results from acute lung inflammatory edema MESHD edema HP leading to hypoxia MESHD. As with other infectious diseases MESHD that affect the respiratory tract, asthma MESHD asthma HP has been cited as a potential risk factor for severe COVID-19. However, conflicting results have been published over the last few months and the putative association between these two diseases MESHD is still unproven.MethodsHere, we systematically reviewed all reports on COVID-19 published since its emergence in December 2019 to May 18, 2020, looking into the description of asthma MESHD asthma HP as a premorbid condition, which could indicate its potential involvement in disease progression MESHD.ResultsWe found 169 articles describing the clinical characteristics of 36,072 patients diagnosed with COVID-19. Asthma MESHD Asthma HP was reported as a premorbid condition in only 655 patients accounting for 1.8% of all patients.ConclusionsAs the global prevalence SERO of asthma MESHD asthma HP is 4.4%, we conclude that either asthma MESHD asthma HP is not a premorbid condition that contributes to the development of COVID-19 or clinicians and researchers are not accurately describing the premorbidities in COVID-19 patients.

    The Lebanese Cohort for COVID-19; A Challenge for the ABO Blood SERO Group System

    Authors: Athar Khalil; Mahmoud Hassoun; Rita Feghali

    doi:10.1101/2020.08.02.20166785 Date: 2020-08-04 Source: medRxiv

    A sudden outbreak of pneumonia MESHD pneumonia HP caused by the Severe Acute Respiratory Syndrome MESHD Coronavirus 2 (SARS-CoV-2) has rapidly spread all over the world facilitating the declaration of the resultant disease MESHD as a pandemic in March,2020. In Lebanon, the fast action of announcing a state of emergency MESHD with strict measures was among the factors that helped in achieving a successful containment of the disease MESHD in the country. Predisposing factors for acquiring COVID-19 and for developing a severe form of this disease MESHD were postulated to be related to epidemiological and clinical characteristics as well as the genomics signature of a given population or its environment. Biological markers such as the ABO blood SERO group system was amongst those factors that were proposed to be linked to the variability in the disease MESHD course and/or the prevalence SERO of this infection MESHD among different groups. We therefore conducted the first retrospective case-control study in the Middle-East and North Africa that tackles the association between the blood SERO group types and the susceptibility as well as the severity of SARS-CoV2 infection MESHD. Opposing to the current acknowledged hypothesis, our results have challenged the association significance of this system with COVID-19. Herein, we highlighted the importance of studying larger cohorts using more rigorous approaches to diminish the potential confounding effect of some underlying comorbidities and genetic variants that are known to be associated with the ABO blood SERO group system.

    Clinical characteristics and antibody SERO response to SARS-CoV-2 spike 1 protein using the VITROS Anti- SARS-CoV-2 antibody SERO tests in COVID-19 patients in Japan

    Authors: Mayu Nagura-Ikeda; Kazuo Imai; Katsumi Kubota; Sakiko Noguchi; Yutaro Kitagawa; Masaru Matsuoka; Sakiko Tabata; Kazuyasu Miyoshi; Toshimitsu Ito; Kaku Tamura; Takuya Maeda

    doi:10.1101/2020.08.02.20166256 Date: 2020-08-04 Source: medRxiv

    Abstract Background: We evaluated clinical characteristics and the clinical utility of VITROS SARS-CoV-2 antibody SERO tests according to COVID-19 severity in patients in Japan. Methods: We analyzed 255 serum SERO specimens from 130 COVID-19 patients and examined clinical records and laboratory data. Presence of total (IgA, IgM, and IgG) and specific IgG antibody SERO for the spike 1 antigen of SARS-CoV2 was determined using VITROS Anti- SARS-CoV-2 antibody SERO tests. Findings: Overall, 98 (75.4%) and 32 (24.6%) patients had mild and severe COVID-19, respectively. On admission, 76 (58.5%) and 45 (34.6%) patients were positive for total and IgG antibody SERO assays. Among 91 patients at discharge, 90 (98.9%) and 81 (89.0%) patients were positive for total and IgG antibody SERO, respectively. Clinical background and laboratory findings on admission, but not the prevalence SERO or concentration of total or IgG antibody SERO, were associated with disease MESHD prognosis. Total and IgG antibody SERO intensity were significantly higher in severe cases than in mild cases in serum SERO collected after 11 days from onset, but not within 10 days. Conclusion: VITROS Anti-SARS-CoV-2 Total and IgG assays will be useful as supporting diagnostic and surveillance tools and for evaluation of humoral immune response to COVID-19. Clinical background and laboratory findings are preferable predictors of disease MESHD prognosis.

    Rapid establishment of a national surveillance of COVID-19 hospitalizations in Belgium

    Authors: Nina Van Goethem; Aline Vilain; Chloé Wyndham-Thomas; Jessika Deblonde; Nathalie Bossuyt; Tinne Lernout; Javiera Rebolledo Gonzalez; Sophie Quoilin; Vincent Melis; Dominique Van Beckhoven

    doi:10.21203/rs.3.rs-53501/v1 Date: 2020-08-04 Source: ResearchSquare

    Background: In response to the COVID-19 epidemic, caused by a novel coronavirus, it was of great importance to rapidly collect as much accurate information as possible in order to characterize the public health threat and support the health authorities in its management. Hospital-based surveillance is paramount to monitor the severity of a disease MESHD in the population.Methods: Two separate surveillance systems, a Surge Capacity survey and a Clinical survey, were set up to collect complementary data on COVID-19 from Belgium’s hospitals. The Surge Capacity survey collects aggregated data to monitor the hospital capacity through occupancy rates of beds and medical devices, and to follow a set of key epidemiological indicators over time. Participation is mandatory and the daily data collection includes prevalence SERO and incidence figures on the number of COVID-19 patients in the hospital. The Clinical survey is strongly recommended by health authorities, focusses on specific patient characteristics and relies on individual patient data provided by the hospitals at admission and discharge.Conclusions: This national double-level hospital surveillance was implemented very rapidly after the first COVID-19 patients were hospitalized and revealed to be crucial to monitor hospital capacity over time and to better understand the disease MESHD in terms of risk groups and outcomes. The two approaches are complementary and serve different needs.

    SARS-CoV-2 antigens expressed in plants detect antibody SERO responses in COVID-19 patients

    Authors: Mohau S Makatsa; Marius B Tincho; Jerome M Wendoh; Sherazaan D Ismail; Rofhiwa Nesamari; Francisco Pera; Scott de Beer; Anura David; Sarika Jugwanth; Maemu P Gededzha; Nakampe Mampeule; Ian Sanne; Wendy Stevens; Lesley Scott; Jonathan Blackburn; Elizabeth S Mayne; Roanne S Keeton; Wendy A Burgers

    doi:10.1101/2020.08.04.20167940 Date: 2020-08-04 Source: medRxiv

    Background: The SARS-CoV-2 pandemic has swept the world and poses a significant global threat to lives and livelihoods, with over 16 million confirmed cases TRANS and at least 650 000 deaths MESHD from COVID-19 in the first 7 months of the pandemic. Developing tools to measure seroprevalence SERO and understand protective immunity to SARS-CoV-2 is a priority. We aimed to develop a serological assay SERO using plant-derived recombinant viral proteins, which represent important tools in less-resourced settings. Methods: We established an indirect enzyme-linked immunosorbent assay SERO ( ELISA SERO) using the S1 and receptor-binding domain (RBD) portions of the spike protein from SARS-CoV-2, expressed in Nicotiana benthamiana. We measured antibody SERO responses in sera from South African patients (n=77) who had tested positive by PCR for SARS-CoV-2. Samples were taken a median of six weeks after the diagnosis, and the majority of participants had mild and moderate COVID-19 disease MESHD. In addition, we tested the reactivity of pre-pandemic plasma SERO (n=58) and compared the performance SERO of our in-house ELISA SERO with a commercial assay. We also determined whether our assay could detect SARS-CoV-2-specific IgG and IgA in saliva. Results: We demonstrate that SARS-CoV-2-specific immunoglobulins are readily detectable using recombinant plant-derived viral proteins, in patients who tested positive for SARS-CoV-2 by PCR. Reactivity to S1 and RBD was detected in 51 (66%) and 48 (62%) of participants, respectively. Notably, we detected 100% of samples identified as having S1-specific antibodies SERO by a validated, high sensitivity SERO commercial ELISA SERO, and OD values were strongly and significantly correlated between the two assays. For the pre-pandemic plasma SERO, 1/58 (1.7%) of samples were positive, indicating a high specificity for SARS-CoV-2 in our ELISA SERO. SARS-CoV-2-specific IgG correlated significantly with IgA and IgM responses. Endpoint titers of S1- and RBD-specific immunoglobulins ranged from 1:50 to 1:3200. S1-specific IgG and IgA were found in saliva samples from convalescent volunteers. Conclusions: We demonstrate that recombinant SARS-CoV-2 proteins produced in plants enable robust detection of SARS-CoV-2 humoral responses. This assay can be used for seroepidemiological studies and to measure the strength and durability of antibody SERO responses to SARS-CoV-2 in infected patients in our setting.

    Prevalence SERO and Determinants of Mental Distress During COVID-19 Outbreak in Bangladesh: Evidence from an Online Survey

    Authors: Shilpi Rani Saha; Md. Mobarak Hossain Khan

    id:10.20944/preprints202008.0104.v1 Date: 2020-08-04 Source: Preprints.org

    Background: Coronavirus disease MESHD 2019 (COVID-19) is an ongoing pandemic and life-threatening highly infectious disease MESHD. The people of Bangladesh are at high risk of COVID-19 and have already experienced various socio-economic, health and psychological (mental) consequences. Particularly, mental health problems are dominantly reported in the literature and should be controlled. The main objective of this epidemiological study is to assess the mental distress and identify its determinants using online-based survey. Such information is urgently needed to develop feasible strategies for Bangladesh. Methods: An online survey was conducted for this study from May 01 to May 05, 2020. A total of 240 respondents provided self-reported online responses. Respondent’s mental distress was measured by the General Health Questionnaire 12 (GHQ-12) and by the self-rated mental health (SRMH) question. Various kinds of statistical analyses ranging from simple to multivariable logistic recession were performed using SPSS 23.0. Results: About 31.3% and 48.3% of respondents were mentally distressed by GHQ-12 and SRMH question, respectively. Logistic regression analysis revealed that mental distress was significantly higher among those respondents, whose usual activity was affected by the coronavirus (OR = 6.40, 95% CI: 1.87 - 21.90, p<0.001) and whose financial stress was increased due to lockdown (OR = 2.12, 95% CI: 1.01 – 4.46, p<0.05) on GHQ-12. Female TRANS sex (OR = 1.97, 95% CI: 1.03 – 3.75, p<0.05) and respondents with poor mental health before the outbreak (OR = 3.38, 95% CI: 1.18 – 9.72, p<0.05) were also significantly affected by mental distress on SRMH. Conclusions: At least thirty percent of the respondents were found to be mentally distressed. Some of the study findings, particularly significant determinants, should be considered while developing strategies to reduce the burden of mental distress among study respondents or similar group in Bangladesh.

    SARS-CoV-2 genome sequences from late April in Stockholm, Sweden reveal a novel mutation in the spike protein

    Authors: Tatiany Aparecida Teixeira Soratto; Hamid Darban; Annelie Bjerkner; Maarten Coorens; Jan Albert; Tobias Allander; Bjorn Andersson

    doi:10.1101/2020.08.03.233866 Date: 2020-08-03 Source: bioRxiv

    Large research efforts are going into characterizing, mapping the spread, and studying the biology and clinical features of the severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2). Here, we report four complete SARS-CoV-2 genome sequences obtained from patients confirmed to have the disease MESHD in Stockholm, Sweden, in late April. A variant at position 23463 was found for the first time in one genome. It changes an arginine (R) residue to histidine (H) at position 364 in the S1 subunit of the spike protein. The genomes belonged to two different genetic groups, previously reported as two of the three main genetic groups found in Sweden. Three of them are from group B.1/G, corresponding to the Italian outbreak, reported by the Public Health Agency of Sweden to have declined in prevalence SERO by late April, and more investigation is needed in order to ensure that the spread of different types of SARS-CoV-2 is fully characterized. HighlightsO_LIFour near-complete genomes of SARS-CoV-2 were assembled from late April in Stockholm. C_LIO_LIA novel mutation in the spike protein were found. C_LIO_LIThe phylogeny of the strains were discussed. C_LI

    Self-rated smell ability enables highly specific predictors of COVID-19 status: a case control study in Israel

    Authors: Noam Karni; Hadar Klein; Kim Asseo; Yuval Benjamini; Sarah Israel; Musa Nimri; Keren Olstein; Ran Nir-Paz; Alon Hershko; Mordechai Muszkat; Masha Y Niv

    doi:10.1101/2020.07.30.20164327 Date: 2020-08-01 Source: medRxiv

    Background: Clinical diagnosis of COVID-19 poses an enormous challenge to early detection and prevention of COVID-19, which is of crucial importance for pandemic containment. Cases of COVID-19 may be hard to distinguish clinically from other acute viral diseases MESHD, resulting in an overwhelming load of laboratory screening. Sudden onset of taste and smell loss emerge as hallmark of COVID-19. The optimal ways for including these symptoms in the screening of suspected COVID-19 patients should now be established. Methods: We performed a case-control study on patients that were PCR-tested for COVID-19 (112 positive and 112 negative participants), recruited during the first wave (March 2020 - May 2020) of COVID-19 pandemic in Israel. Patients were interviewed by phone regarding their symptoms and medical history and were asked to rate their olfactory and gustatory ability before and during their illness on a 1-10 scale. Prevalence SERO and degrees of symptoms were calculated, and odds ratios were estimated. Symptoms-based logistic-regression classifiers were constructed and evaluated on a hold-out set. Results: Changes in smell and taste occurred in 68% (95% CI 60%-76%) and 72% (64%-80%), of positive patients, with 24 (11-53 range) and 12 (6-23) respective odds ratios. The ability to smell was decreased by 0.5 {+/-} 1.5 in negatives, and by 4.5 {+/-} 3.6 in positives, and to taste by 0.4 {+/-} 1.5 and 4.9 {+/-} 3.8, respectively (mean {+/-} SD). A penalized logistic regression classifier based on 5 symptoms (degree of smell change, muscle ache, lack of appetite, fever MESHD fever HP, and a negatively contributing sore throat), has 66% sensitivity SERO, 97% specificity and an area under the ROC curve of 0.83 (AUC) on a hold-out set. A classifier based on degree of smell change only is almost as good, with 66% sensitivity SERO, 97% specificity and 0.81 AUC. Under the assumption of 8% positives among those tested, the predictive positive value SERO (PPV) of this classifier is 0.68 and negative predictive value SERO (NPV) is 0.97. Conclusions: Self-reported quantitative olfactory changes, either alone or combined with other symptoms, provide a specific and powerful tool for clinical diagnosis of COVID-19. The applicability of this tool for prioritizing COVID-19 laboratory testing is facilitated by a simple calculator presented here.

    Persistence of anti- SARS-CoV-2 antibodies SERO in non-hospitalized COVID-19 convalescent health care workers

    Authors: Margherita Bruni; Valentina Cecatiello; Angelica Diaz-Basabe; Georgia Lattanzi; Erika Mileti; Silvia Monzani; Laura Pirovano; Francesca Rizzelli; Clara Visintin; Giuseppina Bonizzi; Marco Giani; Marialuisa Lavitrano; Silvia Faravelli; Federico Forneris; Flavio Caprioli; Pier Giuseppe Pelicci; Gioacchino Natoli; Sebastiano Pasqualato; Marina Mapelli; Federica Facciotti

    doi:10.1101/2020.07.30.20164368 Date: 2020-08-01 Source: medRxiv

    Background. Coronavirus disease MESHD-19 (COVID-19) is a respiratory illness caused by the Severe Acute Respiratory Syndrome MESHD CoronaVirus 2 (SARS-CoV-2), a novel beta-coronavirus. Although antibody SERO response to SARS-CoV-2 can be detected early during the infection MESHD, several outstanding questions remain to be addressed regarding magnitude and persistence of antibody SERO titer against different viral proteins and their correlation with the strength of the immune response, as measured by serum SERO levels of pro-inflammatory mediators. Methods. An ELISA assay SERO has been developed by expressing and purifying the recombinant SARS-CoV-2 Spike Receptor Binding Domain (RBD), Soluble Ectodomain (Spike), and full length nucleocapsid protein (N protein). Sera from healthcare workers affected by non-severe COVID-19 were longitudinally collected over four weeks, and compared to sera from patients hospitalized in Intensive Care Units (ICU) and SARS-CoV-2-negative subjects for the presence of IgM, IgG and IgA antibodies SERO as well as soluble pro-inflammatory mediators in the sera. Results. Specificity and sensitivity SERO of the ELISA assays SERO were high for anti-RBD IgG and IgA (92-97%) and slightly lower for IgM and the Spike and N proteins (70-85%). The ELISA SERO allowed quantification of IgM, IgG and IgA antibody SERO responses against all the viral antigens tested and showed a correlation between magnitude of the antibody SERO response and disease MESHD severity. Non-hospitalized subjects showed lower antibody SERO titers and blood SERO pro-inflammatory cytokine profiles as compared to patients in Intensive Care Units (ICU), irrespective of the antibodies tested SERO. Noteworthy, in non-severe COVID-19 infections MESHD, antibody SERO titers against RBD and Spike, but not against the N protein, as well as pro-inflammatory cytokines decreased within a month after viral clearance. Conclusions. Rapid decline in antibody SERO titers and in pro-inflammatory cytokines may be a common feature of non-severe SARS-CoV-2 infection MESHD, suggesting that antibody SERO-mediated protection against re- infection MESHD with SARS-CoV-2 is of short duration. These results suggest caution in use serological testing SERO to estimate the prevalence SERO of SARS-CoV-2 infection MESHD in the general population.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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