Corpus overview


Overview

MeSH Disease

Human Phenotype

Pneumonia (132)

Fever (126)

Cough (104)

Hypertension (76)

Fatigue (47)


Transmission

Seroprevalence
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    IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection MESHD

    Authors: Bruce A. Rosa; Mushtaq Ahmed; Dhiraj K. Singh; Jose Alberto Choreno-Parra; Journey Cole; Luis Armando Jimenez-Alvarez; Tatiana Sofia Rodriguez-Reyna; Bindu Singh; Olga Golzalez; Ricardo Carrion; Larry S. Schlesinger; John Martin; Joaquin Zuniga; Makedonka Mitreva; Shabaana A Khader; Deepak Kaushal

    doi:10.1101/2020.08.06.239798 Date: 2020-08-06 Source: bioRxiv

    The novel virus SARS-CoV-2 has infected more than 14 million people worldwide resulting in the Coronavirus disease MESHD 2019 (COVID-19). Limited information on the underlying immune mechanisms that drive disease MESHD or protection during COVID-19 severely hamper development of therapeutics and vaccines. Thus, the establishment of relevant animal models that mimic the pathobiology of the disease MESHD is urgent. Rhesus macaques infected with SARS-CoV-2 exhibit disease MESHD pathobiology similar to human COVID-19, thus serving as a relevant animal model. In the current study, we have characterized the transcriptional signatures induced in the lungs of juvenile and old rhesus macaques following SARS-CoV-2 infection MESHD. We show that genes associated with Interferon (IFN) signaling, neutrophil degranulation and innate immune pathways are significantly induced in macaque infected lungs, while pathways associated with collagen formation are downregulated. In COVID-19, increasing age TRANS is a significant risk factor for poor prognosis and increased mortality. We demonstrate that Type I IFN and Notch signaling pathways are significantly upregulated in lungs of juvenile infected macaques when compared with old infected macaques. These results are corroborated with increased peripheral neutrophil counts and neutrophil lymphocyte ratio in older individuals with COVID-19 disease MESHD. In contrast, pathways involving VEGF are downregulated in lungs of old infected macaques. Using samples from humans with SARS-CoV-2 infection MESHD and COVID-19, we validate a subset of our findings. Finally, neutrophil degranulation, innate immune system and IFN gamma signaling pathways are upregulated in both tuberculosis MESHD and COVID-19, two pulmonary diseases MESHD where neutrophils are associated with increased severity. Together, our transcriptomic studies have delineated disease MESHD pathways to improve our understanding of the immunopathogenesis of COVID-19 to facilitate the design of new therapeutics for COVID-19.

    Serology assessment of antibody SERO response to SARS-CoV-2 in patients with COVID-19 by rapid IgM/IgG antibody test SERO

    Authors: Yang De Marinis; Torgny Sunnerhagen; Pradeep Bompada; Anna Blackberg; Runtao Yang; Joel Svensson; Ola Ekstrom; Karl-Fredrik Eriksson; Ola Hansson; Leif Groop; Isabel Goncalves; Magnus Rasmussen

    doi:10.1101/2020.08.05.20168815 Date: 2020-08-06 Source: medRxiv

    The coronavirus disease MESHD 2019 (COVID-19) pandemic has created a global health- and economic crisis. Lifting confinement restriction and resuming to normality depends greatly on COVID-19 immunity screening. Detection of antibodies SERO to severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) which causes COVID-19 by serological methods is important to diagnose a current or resolved infection MESHD. In this study, we applied a rapid COVID-19 IgM/IgG antibody test SERO and performed serology assessment of antibody SERO response to SARS-CoV-2. In PCR-confirmed COVID-19 patients (n=45), the total antibody SERO detection rate is 92% in hospitalized patients and 79% in non-hospitalized patients. We also studied antibody SERO response in relation to time after symptom onset TRANS and disease MESHD severity, and observed an increase in antibody SERO reactivity and distinct distribution patterns of IgM and IgG following disease progression MESHD. The total IgM and IgG detection is 63% in patients with < 2 weeks from disease MESHD onset; 85% in non-hospitalized patients with > 2 weeks disease MESHD duration; and 91% in hospitalized patients with > 2 weeks disease MESHD duration. We also compared different blood SERO sample types and suggest a potentially higher sensitivity SERO by serum SERO/ plasma SERO comparing with whole blood SERO measurement. To study the specificity of the test, we used 69 sera/ plasma SERO samples collected between 2016-2018 prior to the COVID-19 pandemic, and obtained a test specificity of 97%. In summary, our study provides a comprehensive validation of the rapid COVID-19 IgM/IgG serology test, and mapped antibody SERO detection patterns in association with disease MESHD progress and hospitalization. Our study supports that the rapid COVID-19 IgM/IgG test may be applied to assess the COVID-19 status both at the individual and at a population level.

    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.

    General public Knowledge of coronavirus disease MESHD 2019 (COVID-19) at early stages of the pandemic: results of a random online survey in the Kingdom of Saudi Arabia

    Authors: Ali Alqahtani; V Krishnaraju; Mona Alqarni; Mohammed Al-Sheikh Hassan

    doi:10.21203/rs.3.rs-54864/v1 Date: 2020-08-06 Source: ResearchSquare

    AbstractBackground: A novel coronavirus was identified at the end of 2019 in Wuhan City, China. Later, the World Health Organization (WHO) named the disease MESHD caused by the virus coronavirus disease MESHD 2019 (COVID-19) and declared a pandemic in March 2020. Saudi and global health agencies have provided various COVID-19 knowledge tools and facts to the general public. Therefore, this study aims to assess COVID-19 knowledge among the general public in Saudi Arabia at the early stages of the pandemic, including knowledge of prevention practices, home quarantine measures, and compliance with governmental restrictions.Subjects and methods: A cross-sectional study was conducted in March 2020 during the COVID-19 pandemic in Saudi Arabia. The study included 1006 participants who responded to a random online COVID-19 public knowledge questionnaire that included five sections: demographic characteristics, general knowledge, prevention practices, home quarantine measures, and knowledge of governmental restrictions. Data were collected from a random sample recruited through the circulation of the questionnaire on social media platforms and were then analysed by descriptive statistical methods. Three levels of knowledge were established: excellent, intermediate, and poor. Differences in the percentages of participants with different knowledge levels by the demographic variables were analysed using the chi-square test.Results: Regarding overall general knowledge of COVID-19, 75%, 24%, and 1% of the participants had excellent, intermediate, and poor knowledge levels, respectively. Knowledge levels were significantly different by nationality and age TRANS (P=0.027 and 0.008, respectively). The majority of participants (98.4%) reported excellent knowledge of prevention practices, with no statistically significant differences among groups (P>0.005). Older age groups TRANS reported higher knowledge of home quarantine measures (86.6% and 86.4% of the 51-60 and older than 60 age groups TRANS, respectively, P=0.001). Approximately 50% of Saudis reported excellent knowledge of the restrictions imposed by the Saudi government to control the spread of COVID-19, while approximately 45% of non-Saudis had an excellent level of knowledge (P= 0.009).Conclusion and recommendations: High levels of knowledge about the virus, including prevention practices, are essential. The provision of COVID-19 facts and knowledge tools should be focused on younger generations to enhance compliance with the governmental restrictions required to stop the spread of COVID-19.

    Is There a Relationship Between Climate, Morphology and Urbanization and COVID19? Preliminary Analysis of Environmental and Pandemic Data in the Lombardy Region (Northern Italy)

    Authors: Massimiliano Fazzini; Claudio Bna; Alessandro Cecili; Andrea Giuliacci; Sonia Illuminati; Fabrizio Pregliasco; Claudia Baresi; Enrico Miccadei

    id:10.20944/preprints202008.0163.v1 Date: 2020-08-06 Source: Preprints.org

    The coronavirus disease MESHD 2019 (COVID-19) pandemic is the defining global health and socioeconomic crisis of our time and represents the greatest challenge faced by the world since the end of the Second World War. The academic literature indicates that climatic features, specifically the temperature and absolute humidity, are very important factors affecting infectious pulmonary disease MESHD epidemics (e.g., SARS, MERS); however, the influence of climatic parameters on COVID-19 remains extremely controversial. The goal of this study is to quantify the existing relationship between several daily climate parameters (temperature, relative humidity, accumulated precipitation, solar radiation, wind direction and intensity, and evaporation), local morphological parameters, and new daily positive swabs for COVID-19, which represents the only parameter that can be statistically used to quantify the pandemic. The daily deaths MESHD parameter was not considered because it is not reliable due to frequent administrative errors. Daily data on meteorological conditions and new cases of COVID-19 were collected for the Lombardy area from March 1, 2020, to April 20, 2020. This region in Italy exhibited the largest number of official deaths MESHD in the world per million inhabitants, with a value of approximately 1700 per million on june 30, 2020. Moreover, the apparent lethality was approximately 17% in this area, mainly due to the considerable housing density and the extensive presence of industrial and craft areas. The Mann-Kendall test and multivariate statistical analysis showed that none of the considered climatic variables exhibited statistically significant relationships with the epidemiological evolution of COVID-19, at least in the spring months in temperate subcontinental climate areas, with the exception of solar radiation, which was directly related and showed an otherwise low explained variability of approximately 20%. Furthermore, the average temperatures of two highly representative meteorological stations of Molise and Lucania, the most weakly affected by the pandemic. The temperatures at these stations were approximately 1.5°C lower than that in the cities in Lombardy of Bergamo and Brescia, again confirming that a significant relationship between the increase in temperature and decrease in virology from COVID-19 was not evident, at least in the Italian peninsula.

    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.

    Analysis of the potential impact of genomic variants in SARS-CoV-2 genomes from India on molecular diagnostic assays

    Authors: Abhinav Jain; Mercy Rophina; Saurabh Mahajan; Bhavya Balaji Krishnan; Manasa Sharma; Sreya Mandal; Teresa Fernandez; Sumayra Sultanji; Samatha Mathew; Sridhar Sivasubbu; Vinod Scaria

    doi:10.1101/2020.08.05.238618 Date: 2020-08-05 Source: bioRxiv

    An isolated epidemic of Severe Acute Respiratory Syndrome MESHD Coronavirus 2 (SARS-CoV-2) causing Coronavirus Diseases MESHD (C0VID-19) originating in Wuhan, China has now rapidly emerged into a global pandemic affecting millions of people worldwide. Molecular detection of SARS-CoV-2 using reverse transcription polymerase chain reaction (RT-PCR) forms the mainstay in screening, diagnosis and epidemiology of disease MESHD. The virus has been evolving through base substitutions. The recent availability of genomes of SARS-CoV-2 isolates from different countries including India motivated us to assess the presence and potential impact of variations in target sites for the oligonucleotide primers and probes used in molecular diagnosis. We catalogued a total of 132 primers or probes sequences from the literature and the public domain. Our analysis revealed a total of 125 unique genetic variants in 80 either primers or probes binding sites. A total of 13 unique variants had allele frequency of [≥] 1% in Indian SARS-CoV-2 genomes mapped to the primers or probes binding sites. A total of 15 primers or probes binding sites had cumulative variant frequency of [≥] 1% in the SARS-CoV-2 genomes. These included primers or probes sites which are widely used in India and across the world for molecular diagnosis as well as approved by national and international agencies. This highlights the need for sequencing genomes of emerging pathogens to make evidence based policies for development and approval of diagnostics. To the best of our knowledge, ours is the most comprehensive analysis of genomic variants in genomes of SARS-CoV-2 isolates from India and their potential impact on efficacy of molecular diagnostics. Keywords: COVID-19, genomes, SARS-CoV-2, variations, reverse transcription polymerase chain reaction, Gibbs free energy

    A distinct innate immune signature marks progression from mild to severe COVID-19

    Authors: Stéphane Chevrier; Yves Zurbuchen; Carlo Cervia; Sarah Adamo; Miro E Raeber; Natalie de Souza; Sujana Sivapatham; Andrea Jacobs; Esther Bächli; Alain Rudiger; Melina Stüssi-Helbling; Lars C Huber; Dominik J Schaer; Jakob Nilsson; Onur Boyman; Bernd Bodenmiller

    doi:10.1101/2020.08.04.236315 Date: 2020-08-04 Source: bioRxiv

    Coronavirus disease MESHD 2019 (COVID-19) manifests with a range of severities, but immune signatures of mild and severe disease MESHD are still not fully understood. Excessive inflammation MESHD has been postulated to be a major factor in the pathogenesis of severe COVID-19 and innate immune mechanisms are likely to be central in the inflammatory response. We used 40-plex mass cytometry and targeted serum SERO proteomics to profile innate immune cell populations from peripheral blood SERO of patients with mild or severe COVID-19 and healthy controls. Sampling at different stages of COVID-19 allowed us to reconstruct a pseudo-temporal trajectory of the innate immune response. Despite the expected patient heterogeneity, we identified consistent changes during the course of the infection MESHD. A rapid and early surge of CD169+ monocytes associated with an IFN{gamma}+MCP-2+ signature quickly followed symptom onset TRANS; at symptom onset TRANS, patients with mild and severe COVID-19 had a similar signature, but over the course of the disease MESHD, the differences between patients with mild and severe disease MESHD increased. Later in the disease MESHD course, we observed a more pronounced re-appearance of intermediate/non-classical monocytes and mounting systemic CCL3 and CCL4 levels in patients with severe disease MESHD. Our data provide new insights into the dynamic nature of the early inflammatory response to severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) infection MESHD and identifies sustained pathological innate immune responses as a likely key mechanism in severe COVID-19, further supporting investigation of targeted anti-inflammatory interventions in severe COVID-19.

    Epidemiological characteristics of SARS-COV-2 in Myanmar

    Authors: Aung Min Thway; Htun Tayza; Tun Tun Win; Ye Minn Tun; Moe Myint Aung; Yan Naung Win; Kyaw M Tun

    doi:10.1101/2020.08.02.20166504 Date: 2020-08-04 Source: medRxiv

    Coronavirus disease MESHD (COVID-19) is an infectious disease MESHD caused by a newly discovered severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2). In Myanmar, first COVID-19 reported cases were identified on 23rd March 2020. There were 336 reported confirmed cases TRANS, 261 recovered and 6 deaths MESHD through 13th July 2020. The study was a retrospective case series and all COVID-19 confirmed cases TRANS from 23rd March to 13th July 2020 were included. The data series of COVID-19 cases were extracted from the daily official reports of the Ministry of Health and Sports (MOHS), Myanmar and Centers for Disease MESHD Control and Prevention (CDC), Myanmar. Among 336 confirmed cases TRANS, there were 169 cases with reported transmission TRANS events. The median serial interval TRANS was 4 days (IQR 3, 2-5) with the range of 0 - 26 days. The mean of the reproduction number TRANS was 1.44 with (95% CI = 1.30-1.60) by exponential growth method and 1.32 with (95% CI = 0.98-1.73) confident interval by maximum likelihood method. This study outlined the epidemiological characteristics and epidemic parameters of COVID-19 in Myanmar. The estimation parameters in this study can be comparable with other studies and variability of these parameters can be considered when implementing disease MESHD control strategy in Myanmar.

    Characteristics of COVID-19 fatality cases in East Kalimantan, Indonesia

    Authors: Swandari Paramita; Ronny Isnuwardana; Krispinus Duma; Rahmat Bakhtiar; Muhammad Khairul Nuryanto; Riries Choiru Pramulia Yudia; Evi Fitriany; Meiliati Aminyoto

    doi:10.1101/2020.08.01.20166470 Date: 2020-08-04 Source: medRxiv

    Introduction. Coronavirus Disease MESHD (COVID-19) is caused by SARS-CoV-2 infection MESHD. On March 2, 2020, Indonesia announced the first confirmed cases TRANS of COVID-19 infection MESHD. East Kalimantan will play an important role as the new capital of Indonesia. There is attention to the preparedness of East Kalimantan to respond to COVID-19. We report the characteristics of COVID-19 fatality cases in here. Methods. We retrospectively analyzed the fatality cases of COVID-19 patients from the East Kalimantan Health Office information system. All patients were confirmed COVID-19 by RT-PCR examination. Results. By July 31, 2020, 31 fatality cases of patients had been identified as having confirmed COVID-19 in East Kalimantan. The mean age TRANS of the patients was 55.1 + 9.2 years. Most of the patients were men (22 [71.0%]) with age TRANS more than 60 years old (14 [45.2%]). Balikpapan has the highest number of COVID-19 fatality cases from all regencies. Hypertension MESHD Hypertension HP was the most comorbidities in the fatality cases of COVID-19 patients in East Kalimantan. Discussion. Older age TRANS and comorbidities still contributed to the fatality cases of COVID-19 patients in East Kalimantan, Indonesia. Hypertension MESHD Hypertension HP, diabetes, cardiovascular disease MESHD, and cerebrovascular disease MESHD were underlying conditions for increasing the risk of COVID-19 getting into a serious condition. Conclusion. Active surveillance for people older than 60 years old and having underlying diseases MESHD is needed for reducing the case fatality rate of COVID-19 in East Kalimantan. Keywords. Comorbidity, fatality cases, COVID-19, Indonesia.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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