Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (6)

ProteinN (2)

NSP16 (1)

NSP5 (1)

ORF1ab (1)


SARS-CoV-2 Proteins
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    IL-33 HGNC expression in response to SARS-CoV-2 correlates with seropositivity in COVID-19 MESHD convalescent individuals

    Authors: Michal A Stanczak; David E Sanin; Petya Apostolova; Gabriele Nerz; Dimitrios Lampaki; Maike Hofmann; Daniel Steinmann; Robert Thimme; Gerhard Mittler; Cornelius F Waller; Edward J Pearce; Erika L Pearce

    doi:10.1101/2020.07.09.20148056 Date: 2020-07-10 Source: medRxiv

    Our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still developing. We investigated seroprevalence and immune responses in subjects professionally exposed to SARS-CoV-2 and their family members (155 individuals; ages 5-79 years). Seropositivity for SARS-CoV-2 spike PROTEIN glycoprotein aligned with PCR results that confirmed previous infection. Anti-spike IgG titers remained high 60 days post-infection and did not associate with symptoms, but spike-specific IgM did associate with malaise and fever MESHD. We found limited household transmission, with children of infected individuals seldomly seropositive, highlighting professional exposure as the dominant route of infection in our cohort. We analyzed PBMCs from a subset of seropositive and seronegative adults. TLR7 HGNC agonist- activation revealed an increased population of IL-6+TNF-IL-1 HGNC{beta}+ monocytes, while SARS-CoV-2 peptide stimulation elicited IL-33 HGNC, IL-6 HGNC, IFNa2 HGNC, and IL-23 HGNC expression in seropositive individuals. IL-33 HGNC correlated with CD4+ T cell activation in PBMCs from convalescent subjects, and was likely due to T cell-mediated effects on IL-33 HGNC- producing cells. IL-33 HGNC is associated with pulmonary infection MESHD and chronic diseases like asthma MESHD and COPD, but its role in COVID-19 MESHD is unknown. Analysis of published scRNAseq data of bronchoalveolar lavage fluid MESHD ( BALF MESHD) from patients with mild to severe COVID-19 MESHD revealed a population of IL-33 HGNC-producing cells that increases with disease. Together these findings show that IL-33 HGNC production is linked to SARS-CoV- 2 infection MESHD and warrant further investigation of IL-33 HGNC in COVID-19 MESHD pathogenesis and immunity.

    Reconstructing the global dynamics of under-ascertained COVID-19 MESHD cases and infections

    Authors: Timothy W Russell; Nick Golding; Joel Hellewell; Sam Abbott; Lawrence Wright; Carl A B Pearson; Kevin van Zandvoort; Christopher I Jarvis; Hamish Gibbs; Yang Liu; Rosalind M Eggo; John W Edmunds; Adam J Kucharski

    doi:10.1101/2020.07.07.20148460 Date: 2020-07-08 Source: medRxiv

    Background: Asymptomatic or subclinical SARS-CoV-2 infections MESHD are often unreported, which means that confirmed case counts may not accurately reflect underlying epidemic dynamics. Understanding the level of ascertainment (the ratio of confirmed symptomatic cases to the true number of symptomatic individuals) and undetected epidemic progression is crucial to informing COVID-19 MESHD response planning, including the introduction and relaxation of control measures. Estimating case ascertainment over time allows for accurate estimates of specific outcomes such as seroprevalence, which is essential for planning control measures. Methods: Using reported data on COVID-19 MESHD cases and fatalities globally, we estimated the proportion of symptomatic cases (i.e. any person with any of fever MESHD >= to 37.5C, cough, shortness of breath MESHD, sudden onset of anosmia MESHD, ageusia or dysgeusia illness MESHD) that were reported in 210 countries and territories, given those countries had experienced more than ten deaths. We used published estimates of the case fatality ratio (CFR) as an assumed baseline. We then calculated the ratio of this baseline CFR to an estimated local delay-adjusted CFR to estimate the level of under-ascertainment in a particular location. We then fit a Bayesian Gaussian process model to estimate the temporal pattern of under-ascertainment. Results: We estimate that, during March 2020, the median percentage of symptomatic cases detected across the 84 countries which experienced more than ten deaths ranged from 2.38% (Bangladesh) to 99.6% (Chile). Across the ten countries with the highest number of total confirmed cases as of 6th July 2020, we estimated that the peak number of symptomatic cases ranged from 1.4 times (Chile) to 17.8 times (France) larger than reported. Comparing our model with national and regional seroprevalence data where available, we find that our estimates are consistent with observed values. Finally, we estimated seroprevalence for each country. Despite low case detection in some countries, our results that adjust for this still suggest that all countries have had only a small fraction of their populations infected as of July 2020. Conclusions: We found substantial under-ascertainment of symptomatic cases, particularly at the peak of the first wave of the SARS-CoV-2 pandemic, in many countries. Reported case counts will therefore likely underestimate the rate of outbreak growth initially and underestimate the decline in the later stages of an epidemic. Although there was considerable under-reporting in many locations, our estimates were consistent with emerging serological data, suggesting that the proportion of each country's population infected with SARS-CoV-2 worldwide is generally low.

    Health-care workers with COVID-19 MESHD living in Mexico City: clinical characterization and related outcomes

    Authors: Neftali Eduardo Antonio-Villa; Omar Yaxmehen Bello-Chavolla; Arsenio Vargas-Vazquez; Carlos A. Fermin-Martinez; Alejandro Marquez-Salinas; Julio Pisanty-Alatorre; Jessica Paola Bahena-Lopez

    doi:10.1101/2020.07.02.20145169 Date: 2020-07-04 Source: medRxiv

    BACKGROUND: Health-care workers (HCWs) have increased risk for SARS-CoV-2 infection MESHD. Information about the prevalence and risk factors for adverse outcomes in HCWs is scarce in Mexico. Here, we aimed to explore prevalence of SARS-CoV-2, symptoms, and risk factors associated with adverse outcomes in HCWs in Mexico City. METHODS: We explored data collected by the National Epidemiological Surveillance System in Mexico City. All cases underwent real-time RT-PCR test. We explored outcomes related to severe COVID-19 MESHD in HCWs and the diagnostic performance of symptoms to detect SARS-CoV-2 infection MESHD in HCWs. RESULTS: As of July 2nd, 2020, 34,263 HCWs were tested for SARS-CoV-2, and 10,925 were confirmed (31.9%). Overall, 4,200 were nurses (38.4%), 3,244 physicians (29.7%), 126 dentists (1.15%) and 3,355 laboratory personnel and other HCWs (30.7%). After follow-up, 992 HCWs required hospitalization (9.08%), 206 developed severe outcomes (1.89%), and 90 required mechanical-ventilatory support (0.82%). Lethality was recorded in 224 (2.05%) cases. Symptoms associated with SARS-CoV-2 positivity were fever MESHD, cough MESHD, malaise, shivering, myalgias MESHD at evaluation but neither had significant predictive value. We also identified 333 asymptomatic SARS-CoV-2 infections MESHD (3.05%). Older HCWs with chronic non-communicable diseases, pregnancy, and severe respiratory symptoms MESHD were associated with higher risk for adverse outcomes. Physicians had higher risk for hospitalization and for severe outcomes compared with nurses and other HCWs. CONCLUSIONS: We report a high prevalence of SARS-CoV-2 in HCWs in Mexico City. No symptomatology can accurately discern HCWs with SARS-CoV-2 infection MESHD. Particular attention should focus on HCWs with risk factors to prevent adverse outcomes and reduce infection risk.

    Possible COVID-19 MESHD recurrence in an older patient: a case report

    Authors: Antoine Garnier-Crussard; Marine Haution; Mathilde Gueret-Du-Manoir; Quitterie Reynaud; Nathalie Freymond; Maude Bouscambert-Duchamp; Anne Conrad; Claire Falandry

    doi:10.21203/ Date: 2020-06-11 Source: ResearchSquare

    Background: Novel coronavirus ( COVID-19 MESHD) pandemic cause by Severe Acute Respiratory Syndrome Coronavirus-2 MESHD (SARS-CoV-2) threatens the world for few months. Few cases of prolonged positivity of viral tests and clinical recurrence of COVID-19 MESHD have been described. We report the case of a 78-year-old woman with metastatic breast cancer MESHD who developed possible COVID-19 MESHD recurrence in a post-acute and rehabilitation unit. Case presentation: A 78-year-old woman with metastatic breast cancer MESHD and hypertension MESHD developed COVID-19 MESHD. After symptom improvement and RT-PCR negativation, she regained symptom ( fever MESHD, fall) and lymphopenia MESHD on Day 26 and we note a turned positive RT-PCR even though she was tested positive for antibody against SARS-CoV-2. After the diagnosis of possible COVID-19 MESHD recurrence, she was transferred back to an acute “ COVID-19 MESHD” unit and she then quickly clinically recovered. Conclusions: This clinical case allows us to discuss the risk of recurrence and possible specific causes in older patients. Moreover, prolonged symptoms and lymphopenia MESHD could be associated to worse outcomes in older patients. Finally, at a collective level, even if traces of virus detected by RT-PCR were not necessarily correlated with the contagiousness, the importance of possible COVID-19 MESHD recurrence in the care pathway for older adults must be taken into account, since they are often surrounded by frail older people.


    Authors: Banu Uygun-Can; Bilge Acar-Bolat

    doi:10.1101/2020.06.06.20123901 Date: 2020-06-07 Source: medRxiv

    We aimed to summarize reliable medical evidence by the meta-analysis of all published retrospective studies that examined data based on the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by clinical symptoms, molecular (RT-PCR) diagnosis and characteristic CT imaging features in pregnant women. MEDLINE PubMed, SCOPUS, ISI Web of Science, Clinical Key, and CINAHL databases were used to select the studies. Then, 384 articles were received, including the studies until 01/MAY/2020. As a result of the full-text evaluation, 12 retrospective articles covering all the data related were selected. A total of 181 pregnant cases with SARS-CoV-2 infection MESHD SARS-CoV-2 infection MESHDs were included in the meta-analysis within the scope of these articles. According to the results, the incidence of fever MESHD was 38.1% (95% CI: 14.2-65%), and cough was 22% (95% CI: 10.8-35.2%) among all clinical features of pregnant cases with SARS-CoV-2 infection MESHD. So, fever MESHD and cough MESHD are the most common symptoms in pregnant cases with SARS-CoV-2 infection MESHD, and 91.8% (95% CI: 76.7-99.9%) of RT-PCR results are positive. Moreover, abnormal CT incidence is 97.9% (95% CI: 94.2-99.9%) positive. No case was death MESHD. However, as this virus spreads globally, it should not be overlooked that the incidence will increase in pregnant women and may be in the risky group. RT-PCR and CT can be used together in an accurate and safe diagnosis. In conclusion, these findings will provide important guidance for current studies regarding the clinical features and correct detection of SARS-CoV-2 infection MESHD in pregnant women, as well as whether it will create emergency tables that will require the use of a viral drug.

    Olfactory transmucosal SARS-CoV-2 invasion as port of Central Nervous System entry in COVID-19 MESHD patients

    Authors: Jenny Meinhardt; Josefine Radke; Carsten Dittmayer; Ronja Mothes; Jonas Franz; Michael Laue; Julia Schneider; Sebastian Bruenink; Olga Hassan; Werner Stenzel; Marc Windgassen,; Larissa Roessler; Hans-Hilmar Goebel; Hubert Martin; Andreas Nitsche; Walter Schulz-Schaeffer; Samy Hakroush; Martin S Winkler; Bjoern Tampe; Sefer Elezkurtaj; David Horst; Lars Oesterhelweg; Michael Tsokos; Barbara Ingold Heppner; Christine Stadelmann; Christian Drosten; Victor M Corman; Helena Radbruch; Frank L Heppner

    doi:10.1101/2020.06.04.135012 Date: 2020-06-04 Source: bioRxiv

    The newly identified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 MESHD, a pandemic respiratory disease MESHD presenting with fever MESHD, cough MESHD, and often pneumonia MESHD. Moreover, thromboembolic MESHD events throughout the body including the central nervous system (CNS) have been described. Given first indication for viral RNA presence in the brain and cerebrospinal fluid and in light of neurological symptoms MESHD in a large majority of COVID-19 MESHD patients, SARS-CoV-2-penetrance of the CNS is likely. By precisely investigating and anatomically mapping oro- and pharyngeal regions and brains of 32 patients dying from COVID-19 MESHD, we not only describe CNS infarction MESHD due to cerebral thromboembolism MESHD, but also demonstrate SARS-CoV-2 neurotropism MESHD. SARS-CoV-2 enters the nervous system via trespassing the neuro-mucosal interface in the olfactory mucosa by exploiting the close vicinity of olfactory mucosal and nervous tissue including delicate olfactory and sensitive nerve endings. Subsequently, SARS-CoV-2 follows defined neuroanatomical structures, penetrating defined neuroanatomical areas, including the primary respiratory and cardiovascular control center in the medulla oblongata.

    Screening and Analysis of COVID-19 MESHD cases in non-epidemic areas: A Retrospective Study

    Authors: Yan Zhu; Yan Guo; Juan Ma; Mao-shi Li; Jia-fei Chen; Ming Liu; Ze-hui Yan; Guo-hong Deng; Qing Mao; Hui-min Liu

    doi:10.21203/ Date: 2020-06-01 Source: ResearchSquare

    Objective: To compare the epidemiological and clinical characteristics of confirmed and suspected corona virus disease MESHD 2019 ( COVID-19 MESHD) cases via the process of “triage-screening-isolation-transfer” in the hospitals of non-epidemic areas.Methods: The general data, epidemiological history, clinical symptoms, laboratory examination, and chest computed tomography (CT) imaging characteristics of 38 patients with suspected COVID-19 MESHD, admitted between January 21 and March 5, 2020, were analyzed.Results: According to the results of the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) ribonucleic MESHD acid (RNA) testing, the patients were divided into study group (RNA positive) and control group (RNA negative). Ultimately, 8 cases were RNA-positive and diagnosed as CDVID-19, and 30 cases were negative. Approximately half of the patients in the study group returned to Chongqing from Wuhan; this number was significantly larger than that of the control group (P<0.05). The number of subjects in close contact with the confirmed cases with SARS-CoV-2 RNA-positive and the incidence of aggregation was significantly larger in the study group than in the control group (both P<0.05). The clinical symptom of the study group was mainly low fever MESHD (with or without cough MESHD). The patients with decreased white blood cells (WBC) in the study group were significantly more than those in the control group (P<0.05). Both group had reduced lymphocytes (Lym) but the number of patients with increased C-reactive protein HGNC ( CRP HGNC) in the study group was significantly more than that in the control group (P<0.05). There were different degrees of chest CT abnormalities MESHD in both study and control group (P > 0.05). Conclusion: The epidemiological investigations in screening for infectious diseases MESHD is crucial. The risk of infection was high from the primary epidemic area and/or in close contact with the confirmed case. The most common form of clustering occurrence was family aggregation. CDVID-19 was mainly characterized by fever MESHD and respiratory symptoms, although asymptomatic infection may also occur. Decreased WBC, decreased Lym, and increased CRP HGNC are common characteristics but can also be combined with other respiratory tract virus infections MESHD. COVID 19 screening by chest CT alone had certain limitations in non- epidemic areas.

    Clinical and biochemical indexes of 11 COVID-19 MESHD patients and the genome sequence analysis of the tested SARS-CoV-2

    Authors: Zhikang Yu; Heming Wu; Qingyan Huang; Xuemin Guo; Zhixiong Zhong

    doi:10.21203/ Date: 2020-05-29 Source: ResearchSquare

    BackgroundAt present, SARS-CoV-2 epidemic MESHD in the world rapidly spread. It is a serious global public health emergency.MethodsHere we described the clinical characteristics of 11 SARS-CoV-2 infected MESHD patients hospitalized in the Meizhou People's Hospital. And viral genome sequences of SARS-CoV-2 from these patients were analyzed.ResultsOf the 11 patients, six cases developed fever MESHD, nine cases developed cough MESHD, and two cases developed headache MESHD and chills. Four patients (36.4%) had underlying diseases. Pneumonia is the most common complication. The laboratory test results showed that there was no adult patients with increased LYM/LYM%. Most patients had normal total protein (TP) and albumin ( ALB HGNC), but only two patients had decreased. Most patients had increased or normal levels of erythrocyte sedimentation rate (ESR), C reactive protein HGNC ( CRP HGNC), activated partial thromboplastin time (APTT), fibrinogen HGNC (FIB), creatine kinase isoenzymes (CK-MB), and lactate dehydrogenase (LDH). Neutrophil (NEU) (r=0.664, P=0.026), CK-MB (r=0.655, P=0.029), blood urea nitrogen (BUN) (r=0.682, P=0.021) and SARS-CoV-2 virus cycle threshold (Ct) value were significantly correlated. Multiple sequence alignment (MSA) shows that we identified two different SNPs at positions 8781 and 28144, and have a completely linked genetic form of 8781C-28144T and 8781T-28144C.ConclusionsThe reports of these 11 cases in our hospital will provide useful information for the diagnosis, treatment and drug development of SARS-CoV-2.

    Benefit-risk analysis of health benefits of routine childhood immunisation against the excess risk of SARS-CoV-2 infection MESHDs during the Covid-19 pandemic MESHD Covid-19 pandemic MESHD in Africa

    Authors: Kaja Abbas; Simon R Procter; Kevin van Zandvoort; Andrew Clark; Sebastian Funk; - LSHTM CMMID Covid-19 Working Group; Tewodaj Mengistu; Dan Hogan; Emily Dansereau; Mark Jit; Stefan Flasche

    doi:10.1101/2020.05.19.20106278 Date: 2020-05-26 Source: medRxiv

    Background: National immunisation programmes globally are at risk of suspension due to the severe health system constraints and physical distancing measures in place to mitigate the ongoing COVID-19 MESHD COVID-19 MESHD pandemic. Our aim is to compare the health benefits of sustaining routine childhood immunisation in Africa against the risk of acquiring SARS-CoV-2 infections MESHD through visiting routine vaccination service delivery points. Methods: We used two scenarios to approximate the child deaths that may be caused by immunisation coverage reductions during COVID-19 MESHD outbreaks. First, we used previously reported country-specific child mortality impact estimates of childhood immunisation for diphtheria, tetanus MESHD, pertussis, hepatitis B MESHD, Haemophilus influenzae type b, pneumococcal MESHD, rotavirus MESHD, measles, meningitis A MESHD, rubella MESHD, and yellow fever MESHD (DTP3, HepB3, Hib3, PCV3, RotaC, MCV1, MCV2, MenA, RCV, YFV) to approximate the future deaths averted before completing five years of age by routine childhood vaccination during a 6-month COVID-19 MESHD risk period without catch-up campaigns. Second, we analysed an alternative scenario that approximates the health benefits of sustaining routine childhood immunisation to only the child deaths averted from measles outbreaks during the COVID-19 MESHD risk period. The excess number of infections due to additional SARS-CoV-2 exposure during immunisation visits assumes that contact reducing interventions flatten the outbreak curve during the COVID-19 MESHD risk period, that 60% of the population will have been infected by the end of that period, that children can be infected by either vaccinators or during transport and that upon child infection the whole household would be infected. Country specific household age structure estimates and age dependent infection fatality rates are then applied to calculate the number of deaths attributable to the vaccination clinic visits. We present benefit-risk ratios for routine childhood immunisation alongside 95% uncertainty range estimates from probabilistic sensitivity analysis. Findings: For every one excess COVID-19 MESHD death attributable to SARS-CoV-2 infections MESHD acquired during routine vaccination clinic visits, there could be 84 (14-267) deaths in children prevented by sustaining routine childhood immunisation in Africa. The benefit-risk ratio for the vaccinated children, siblings, parents or adult care-givers, and older adults in the households of vaccinated children are 85,000 (4,900 - 546,000), 75,000 (4,400 - 483,000), 769 (148 - 2,700), and 96 (14 - 307) respectively. In the alternative scenario that approximates the health benefits to only the child deaths averted from measles outbreaks, the benefit-risk ratio to the households of vaccinated children is 3 (0 - 10) under these highly conservative assumptions and if the risk to only the vaccinated children is considered, the benefit-risk ratio is 3,000 (182 - 21,000). Interpretation: Our analysis suggests that the health benefits of deaths prevented by sustaining routine childhood immunisation in Africa far outweighs the excess risk of COVID-19 MESHD deaths associated with vaccination clinic visits, especially for the vaccinated children. However, there are other factors that must be considered for strategic decision making to sustain routine childhood immunisation in African countries during the COVID-19 pandemic MESHD. These include logistical constraints of vaccine supply chain problems caused by the COVID-19 pandemic MESHD, reallocation of immunisation providers to other prioritised health services, healthcare staff shortages caused by SARS-CoV-2 infections MESHD among the staff, decreased demand for vaccination arising from community reluctance to visit vaccination clinics for fear of contracting SARS-CoV-2 infections MESHD, and infection risk to healthcare staff providing immunisation services as well as to their households and onward SARS-CoV-2 transmission into the wider community.

    COVID-19 MESHD Outcomes in 4712 consecutively confirmed SARS-CoV2 cases in the city of Madrid.

    Authors: Sarah Heili-Frades; Pablo Minguez; Ignacio Mahillo-Fernandez; Tomas Prieto-Rumeau; Antonio Herrero Gonzalez; Lorena de la Fuente; Maria Jesus Rodriguez Nieto; German Peces-Barba Romero; Mario Peces-Barba; Maria del Pilar Carballosa de Miguel; Itziar Fernandez Ormaechea; Alba Naya Prieto; Farah Ezzine de Blas; Luis Jimenez Hiscock; Cesar Perez Calvo; Arnoldo Santos; Luis Enrique Munoz Alameda; Fredeswinda Romero Bueno; Miguel Gorgolas Hernandez-Mora; Alfonso Cabello Ubeda; Beatriz Alvarez Alvarez; Elizabet Petkova; Nerea Carrasco; Dolores Martin Rios; Nicolas Gonzalez Mangado; Olga Sanchez Pernaute

    doi:10.1101/2020.05.22.20109850 Date: 2020-05-25 Source: medRxiv

    There is limited information describing features and outcomes of patients requiring hospitalization for COVID19 MESHD disease and still no treatments have clearly demonstrated efficacy. Demographics and clinical variables on admission, as well as laboratory markers and therapeutic interventions were extracted from electronic Clinical Records (eCR) in 4712 SARS-CoV2 infected MESHD patients attending 4 public Hospitals in Madrid. Patients were stratified according to age and stage of severity. Using multivariate logistic regression analysis, cut-off points that best discriminated mortality were obtained for each of the studied variables. Principal components analysis and a neural network (NN) algorithm were applied. A high mortality incidence associated to age >70, comorbidities ( hypertension MESHD, neurological disorders MESHD and diabetes MESHD), altered vitals such as fever MESHD, heart rhythm disturbances MESHD or elevated systolic blood pressure, and alterations in several laboratory tests. Remarkably, analysis of therapeutic options either taken individually or in combination drew a universal relationship between the use of Cyclosporine A and better outcomes as also a benefit of tocilizumab and/or corticosteroids in critically ill MESHD patients. We present a large Spanish population-based study addressing factors influencing survival in current SARS CoV2 pandemic, with particular emphasis on the effectivity of treatments. In addition, we have generated an NN capable of identifying severity predictors of SARS CoV2. A rapid extraction and management of data protocol from eCR and artificial intelligence in-house implementations allowed us to perform almost real time monitoring of the outbreak evolution.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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