Corpus overview


Overview

MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (1492)

ProteinN (428)

NSP5 (315)

ComplexRdRp (187)

ProteinE (102)


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    Genome-wide CRISPR activation screen identifies novel receptors for SARS-CoV-2 entry MESHD

    Authors: Shiyou Zhu; Ying Liu; Zhuo Zhou; Zhiying Zhang; Xia Xiao; Zhiheng Liu; Ang Chen; Xiaojing Dong; Feng Tian; Shihua Chen; Yiyuan Xu; Chunhui Wang; Qiheng Li; Xuran Niu; Qian Pan; Shuo Du; Junyu Xiao; Jianwei Wang; Wensheng Wei

    doi:10.1101/2021.04.08.438924 Date: 2021-04-09 Source: bioRxiv

    The ongoing pandemic of coronavirus disease 2019 MESHD ( COVID-19 MESHD) caused by severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) has been endangering worldwide public health and economy. SARS-CoV-2 infects MESHD a variety of tissues where the known receptor ACE2 HGNC is low or almost absent, suggesting the existence of alternative pathways for virus entry. Here, we performed a genome-wide barcoded-CRISPRa screen to identify novel host factors that enable SARS-CoV-2 infection MESHD. In addition to known host proteins, i.e PROTEIN. ACE2 HGNC, TMPRSS2 HGNC, and NRP1 HGNC, we identified multiple host components, among which LDLRAD3 HGNC, TMEM30A HGNC, and CLEC4G HGNC were confirmed as functional receptors for SARS-CoV-2. All these membrane proteins bind directly to spike's N-terminal domain ( NTD HGNC). Their essential and physiological roles have all been confirmed in either neuron or liver cells. In particular, LDLRAD3 HGNC and CLEC4G HGNC mediate SARS-CoV-2 entry MESHD and infection in a fashion independent of ACE2 HGNC. The identification of the novel receptors and entry mechanisms could advance our understanding of the multiorgan tropism of SARS-CoV-2, and may shed light on the development of the therapeutic countermeasures against COVID-19 MESHD.

    Behavioural responses to Covid-19 MESHD health certification: A rapid review

    Authors: John Drury; Guanlan Mao; Ann John; Atiya Kamal; James Rubin; Clifford Stott; Tushna Vandrevala; Theresa Marteau

    doi:10.1101/2021.04.07.21255072 Date: 2021-04-09 Source: medRxiv

    Background Covid-status certification (certificates for those who test negative for the SARS-CoV-2 virus, test positive for antibodies, or who have been vaccinated against SARS-CoV-2) has been proposed to enable safer access to a range of activities. Realising these benefits will depend in part upon the behavioural and social impacts of certification. The aim of this rapid review was to describe public attitudes towards certification, and its possible impact on uptake of testing and vaccination, protective behaviours, and crime. Method A search was undertaken in peer-reviewed databases, pre-print databases, and the grey literature, from 2000 to December 2020. Studies were included if they measured attitudes towards or behavioural consequences of health certificates based on one of three indices of Covid-19 MESHD status: test-negative result for current infectiousness, test-positive for antibodies conferring natural immunity, or vaccination(s) conferring immunity. Results Thirty-three papers met the inclusion criteria, only three of which were rated as low risk of bias. Public attitudes were generally favourable towards the use of immunity certificates for international travel, but unfavourable towards their use for access to work and other activities. A significant minority was strongly opposed to the use of certificates of immunity for any purpose. The limited evidence suggested that intention to get vaccinated varied with the activity enabled by certification or vaccination (e.g., international travel). Where vaccination is seen as compulsory this could lead to unwillingness to accept a subsequent vaccination. There was some evidence that restricting access to settings and activities to those with antibody test certificates may lead to deliberate exposure to infection in a minority. Behaviours that reduce transmission may decrease upon health certificates based on any of the three indices of Covid-19 MESHD status, including physical distancing and handwashing. Conclusions The limited evidence suggests that health certification in relation to COVID-19 MESHD (outside of the context of international travel) has the potential for harm as well as benefit. Realising the benefits while minimising the harms will require real-time evaluations allowing modifications to maximise the potential contribution of certification to enable safer access to a range of activities.

    The Value of a Regional Living COVID-19 MESHD Registry and the Challenges of Keeping It Alive

    Authors: John Hanna; Tara Chen; Carlos Portales-Castillo; Donna Newhart; Katherine Schantz; Kathleen Rozzi; Jonathan Bress; Emil Lesho

    doi:10.1101/2021.04.06.21255019 Date: 2021-04-09 Source: medRxiv

    Background: The need for rapid access to regularly updated patient data for hypothesis testing, surge planning, and epidemiologic investigations underscore the value of updated registries that clinicians, researchers, and policy makers can easily access for local and regional planning. We sought to create an adaptive, living registry containing detailed clinical and epidemiologic and outcome data from SARS-CoV-2-PCR-positive patients in our healthcare system. Methods: From 03/13/202 onward, demographics, comorbidities, outpatient medications, along with 75 laboratory, 2 imaging, 19 therapeutic, and 4 outcome-related parameters were manually extracted from the electronic medical record of SARS-CoV-2 positive patients. These parameters were entered on a registry featuring calculation, graphing tools, pivot tables, and a macro programming language. Initially, two internal medicine residents populated the database, then professional data abstractors populated the registry. When the National Center for Immunization and Respiratory Diseases MESHD released their COVID-19 MESHD case report form for public access, we adapted it and used it on a browser-based, metadata-driven electronic data capture software platform. Statistics were performed in R and Minitab. Results: At the time of this submission, 200,807 SARS-CoV-2 RT-PCR tests were performed on 107,604 distinct patients. 3699 (3.4%) of those have had positive results. Of those, 399 (11%) have had the more than 75 parameters full entered in the registry. The average follow-up period was 25 days (range 21-34 days). Age, male gender, diabetes MESHD, hypertension MESHD, cardiovascular disease MESHD, kidney disease MESHD, and cancer MESHD were associated with hospital admission (all p values < 0.01), but not ICU admission. Statin, ACEI-ARB, and acid suppressant use were associated with admission (all p values < 0.03). Obesity MESHD and history of autoimmune disease MESHD were not associated with need for admission. Supplemental oxygen, vasopressor requirement, and outpatient statin use were associated with increased mortality (all p values < 0.03). Conclusion: A living COVID-19 MESHD registry represents a mechanism to facilitate optimal sharing of data between providers, consumers, health information networks, and health plans through technology-enabled, secure-access electronic health information. Our approach also involves a diversity of new roles in the field, such as using residents, staff, and the quality department, in addition to professional data extractors and the health informatics team. However, due to the overwhelming number of infections that continues to accelerate, and the labor/time intense nature of the project, only 11% of all patients with COVID-19 MESHD had all parameters entered in the registry. Therefore, this report also offers lessons learned and discusses sustainability issues, should others wish to establish a registry. It also highlights the local and broader public health significance of the registry.

    Companionship for women using English maternity services during COVID-19 MESHD: National and organisational perspectives

    Authors: Gill Thomson; Marie Clare Balaam; Rebecca Nowland; Nicola Crossland; Gill Moncrieff; Stephanie Heys; Arni Sarian; Joanne Cull; Soo Downe

    doi:10.1101/2021.04.08.21254762 Date: 2021-04-09 Source: medRxiv

    Objectives: To explore the impact of COVID-19 MESHD on companionship for women using maternity services in England, as part of the Achieving Safe and Personalised maternity care In Response to Epidemics (ASPIRE COVID-19 MESHD UK) study. Setting: Maternity care provision in England. Participants: Interviews were held with 26 national governmental, professional, and service-user organisation leads including representatives from the Royal College of Midwives, NHS England, Birthrights and AIMS (July-Dec). Other data included public-facing outputs logged from 25 maternity Trusts (Sept/ Oct HGNC) and data extracted from 78 documents from 8 key governmental, professional and service-user organisations that informed national maternity care guidance and policy (Feb-Dec). Results: Six themes emerged: Postcode lottery of care highlights variations in companionship practices, Confusion MESHD and stress around rules relates to a lack of and variable information concerning companionship, Unintended consequences concerns the negative impacts of restricted companionship on service-users and staff, Need for flexibility highlights concerns about applying companionship policies irrespective of need, Acceptable time for support highlights variations in when and if companionship was allowed antenatally and intrapartum; and Loss of human rights for gain in infection control emphasizes how a predominant focus on infection control was at a cost to psychological safety and womens human rights. Conclusions: Policies concerning companionship have been inconsistently applied within English maternity services during the COVID-19 pandemic MESHD. In some cases, policies were not justified by the level of risk, and were applied indiscriminately regardless of need. This was associated with psychological harms for some women and staff. There is an urgent need to determine how to balance risks and benefits sensitively and flexibly and to optimise outcomes during the current and future crisis situations.

    Intranasal HD MESHD-Ad Vaccine Protects the Upper and Lower Respiratory Tracts of hACE2 HGNC Mice against SARS-CoV-2

    Authors: Huibi Cao; Juntao Mai; Zhichang Zhou; Zhijie Li; Rongqi Duan; Jacqueline Watt; Ziyan Chen; Ranmal Avinash Bandara; Ming Li; Sang Kyun Ahn; Betty Boon; Natasha Christie; Scott Gray-Owen; Rob Kozak; Samira Mubareka; James M Rini; Jim Hu; Jun Liu

    doi:10.1101/2021.04.08.439006 Date: 2021-04-09 Source: bioRxiv

    The COVID-19 pandemic MESHD has affected more than 120 million people and resulted in over 2.8 million deaths worldwide. Several COVID-19 MESHD vaccines have been approved for emergency use in humans and are being used in many countries. However, all of the approved vaccines are administered by intramuscular injection and this may not prevent upper airway infection MESHD or viral transmission. Here, we describe intranasal immunization of a COVID-19 MESHD vaccine delivered by a novel platform, the helper-dependent adenoviral ( HD MESHD-Ad) vector. Since HD MESHD-Ad vectors are devoid of adenoviral coding sequences, they have a superior safety profile and a large cloning capacity for transgenes. The vaccine ( HD MESHD-Ad_RBD) codes for the receptor binding domain (RBD) of the SARS-CoV-2 spike PROTEIN protein and intranasal immunization induced robust mucosal and systemic immunity. Moreover, intranasal immunization of K18- hACE2 HGNC mice with HD MESHD-Ad_RBD using a prime-boost regimen, resulted in complete protection of the upper respiratory tract against SARS-CoV-2 infection MESHD. As such, intranasal immunization based on the HD MESHD-Ad vector promises to provide a powerful platform for constructing highly effective vaccines targeting SARS-CoV-2 and its emerging variants.

    Machine Learning based COVID-19 MESHD Diagnosis from Blood Tests with Robustness to Domain Shifts

    Authors: Theresa Roland; Carl Boeck; Thomas Tschoellitsch; Alexander Maletzky; Sepp Hochreiter; Jens Meier; Guenter Klambauer

    doi:10.1101/2021.04.06.21254997 Date: 2021-04-09 Source: medRxiv

    We investigate machine learning models that identify COVID-19 MESHD positive patients and estimate the mortality risk based on routinely acquired blood tests in a hospital setting. However, during pandemics or new outbreaks, disease and testing characteristics change, thus we face domain shifts. Domain shifts can be caused, e.g., by changes in the disease prevalence (spreading or tested population), by refined RT-PCR testing procedures (taking samples, laboratory), or by virus mutations. Therefore, machine learning models for diagnosing COVID-19 MESHD or other diseases may not be reliable and degrade in performance over time. To countermand this effect, we propose methods that first identify domain shifts and then reverse their negative effects on the model performance. Frequent re-training and re-assessment, as well as stronger weighting of more recent samples, keeps model performance and credibility at a high level over time. Our diagnosis models are constructed and tested on large-scale data sets, steadily adapt to observed domain shifts, and maintain high ROC AUC values along pandemics.

    Prevalence of SARS-CoV-2 antibodies in Denmark: Nationwide, population-based seroepidemiological surveys

    Authors: Laura Espenhain; Siri Tribler; Charlotte Svaerke Joergensen; Christian Holm Hansen; Ute Wolf Sonksen; Steen Ethelberg

    doi:10.1101/2021.04.07.21254703 Date: 2021-04-09 Source: medRxiv

    Background. Seroprevalence studies have proven an important tool to monitor the progression of the coronavirus disease 2019 MESHD ( COVID-19 MESHD) epidemic. We present results of consecutive population-based seroprevalence surveys performed in Denmark in 2020. Methods. Invitation letters including a questionnaire covering symptoms were sent to representatively drawn samples of the population in spring, late summer and autumn/winter of 2020. Blood samples from participants taken at public test-centers were analyzed for total Ig and seroprevalence estimates per population segment calculated and compared to other surveillance parameters. Results. From 34,081 participating individuals (response rate 33%), we obtained seroprevalence estimates increasing from 1.1% (95%CI: 0.7%-1.7) in May to 4.0 % (95%CI: 3.4%-4.7%) in December 2020. By December 2020, 1.5% of the population 12 years and older had tested positive by PCR. Seroprevalence estimates were roughly 3 times higher in those aged 12-29 compared to 65+ and higher in metropolitan municipalities. Among seropositives, loss of taste/smell were the more specific symptoms, 32%-56% did not report any symptoms. In half of seroconverted families, we did not see evidence of transmission between generations. Infected individuals in older age groups were hospitalized several fold more often than in younger. Conclusions. Seroprevalence increased during 2020; younger age groups were primarily infected in the autumn/winter surge. Approximately half were asymptomatically infected. Denmark has a high per capita test rate; roughly two undiagnosed infections of COVID-19 MESHD were estimated to occur for each diagnosed case. The epidemic appears to have progressed relatively modestly during 2020 in Denmark.

    Reopening Italy's Schools MESHD in September 2020: A Bayesian Estimation of the Change in the Growth Rate of New SARS-CoV-2 Cases

    Authors: Luca Casini; Marco Roccetti

    doi:10.1101/2021.04.06.21254993 Date: 2021-04-09 Source: medRxiv

    Abstract Objectives: CoViD-19 MESHD's second wave started a debate on the potential role of schools as a primary factor in the contagion resurgence. Two opposite positions appeared: those convinced that schools played a major role in spreading SARS-CoV-2 infections MESHD SARS-CoV-2 infections MESHD and those who were not. We studied the growth rate of the total number of SARS-CoV-2 infections MESHD in all the Italian regions, before and after the school reopening (September - October 2020), investigating the hypothesis of an association between schools and the resurgence of the virus in Italy. Methods: Using Bayesian piecewise linear regression to scrutinize the number of daily SARS-CoV-2 infections MESHD in each Italian, we looked for an estimate of a changepoint in the growth rate of those confirmed cases. We compared the changepoints with the school opening dates, for each Italian region. The regression allows to discuss the change in steepness of the infection MESHD curve, before and after the changepoint. Results: In 15 out of 21 Italian regions (71%), an estimated change in the rate of growth of the total number of daily SARS-CoV-2 infection MESHD cases occurred after an average of 16.66 days (CI 95% 14.47 to 18.73) since the school reopening. The number of days required for the SARS-CoV-2 daily cases to double went from an average of 47.50 days (CI 95% 37.18 to 57.61) before the changepoint to an average of 7.72 days (CI 95% 7.00 to 8.48) after it. Conclusion: Studying the rate of growth of daily SARS-CoV-2 cases in all the Italian regions provides some evidence in favor of a link between school reopening and the resurgence of the virus in Italy. The number of factors that could have played a role are too many to give a definitive answer. Still, the temporal correspondence warrants for a controlled experiment to clarify how much reopening schools mattered.

    Reduction in the 2020 Life Expectancy in Brazil after COVID-19 MESHD

    Authors: Marcia C. Castro; Susie Gurzenda; Cassio M. Turra; Sun Kim; Theresa Andrasfay; Noreen Goldman

    doi:10.1101/2021.04.06.21255013 Date: 2021-04-09 Source: medRxiv

    Brazil has the second-largest number of COVID-19 MESHD deaths worldwide. We use data on reported deaths to measure and compare the death toll across states from a demographic perspective. We estimate a decline in 2020 life expectancy at birth of 1.94 years, resulting in a mortality level not seen since 2013. The reduction in life expectancy at age 65 was 1.58 years, setting Brazil back to 2009 levels. The decline was larger for males, widening by 2.3% and 5.4% the female-male gap in life expectancy at birth and at age 65, respectively. Among states, Amazonas lost 59.6% of the improvements in life expectancy at birth since 2000. With 2021 COVID-19 MESHD deaths at about 43% of the total 2020 figures (as of mid-March) the demographic effect is likely to be even higher this year.

    Continuous monitoring of SARS-CoV-2 RNA in urban wastewater from Porto, Portugal: sampling and analysis protocols

    Authors: Maria Paola Tomasino; Miguel Semedo; Pedro Vieira; Elza Ferraz; Adelaide Rocha; Maria F. Carvalho; Catarina Magalhaes; Ana P. Mucha

    doi:10.1101/2021.04.06.21254994 Date: 2021-04-09 Source: medRxiv

    Research on the emerging COVID-19 pandemic MESHD is demonstrating that wastewater infrastructures can be used as public health observatories of virus circulation in human communities. Important efforts are being organized worldwide to implement sewage-based surveillance of SARS-CoV-2 that can be used for preventive or early warning purposes, informing preparedness and response measures. However, its successful implementation requires important and iterative methodological improvements, as well as the establishment of standardized methods. The aim of this study was to develop a continuous monitoring protocol for SARS-CoV-2 in wastewater, that could be used to model virus circulation within the communities, complementing the current clinical surveillance. Specific objectives included (1) optimization and validation of a sensitive method for virus quantification; (2) monitoring the time-evolution of SARS-CoV-2 in wastewater from two wastewater treatment plants (WWTPs) in the city of Porto, Portugal. Untreated wastewater samples were collected weekly from the two WWTPs between May 2020 and March 2021, encompassing two COVID-19 MESHD incidence peaks in the region (mid-November 2020 and mid-January 2021). In the first stage of this study, we compared, optimized and selected a sampling and analysis protocol that included RNA virus concentration through centrifugation, RNA extraction from both liquid and solid fractions and quantification by reverse transcription quantitative PCR (RT-qPCR). In the second stage, we used the selected methodology to track SARS-CoV-2 in the collected wastewater over time. SARS-CoV-2 RNA was detected in 39 and 37 out of 48 liquid and solid fraction samples of untreated wastewater, respectively. The copy numbers varied throughout the study between 0 and 0.15 copies/ng RNA and a good fit was observed between the SARS-CoV-2 RNA concentration in the untreated wastewater and the COVID-19 MESHD temporal trends in the study region. In agreement with the recent literature, the results from this study support the use of wastewater-based surveillance to complement clinical testing and evaluate temporal and spatial trends of the current pandemic.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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