COVID-19

A public repository of scientific and media resources of SARS-CoV-2 related COVID-19 maintained by ITER.

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April 13, 2020 updates: few new articles in Scientific Literatura section and MIDAS COVID-19 repository in Data Sources section. As the repository increases its size, we are moving into a Wiki format (soon here!).

Use the "Home" button to move up between sections and the ToC.

Table of contents

• Clinical Trials
• Educational resources
• Genomics of SARS-CoV-2
• Guidelines, Society's Clinical and Professional Statements
• Media sources
• Protocols
• Rapid Tests
• Research Coalitions and Funding Calls
• Respirators, masks, and other Personal Protective Equipments (PPE)
• Scientific Communications and Literature (Pre-prints & Peer-Reviewed Papers)
• Maths and Epidemiological Models
• PCR related articles
• Sciencific Data and Resources
• Autonomous Regions and Cities in Spain
• Sequencing, Sequences and Bioinformatics
• Shiny and R related dashboards and packages. Under construction
• Viral mechanisms: infection, entry, and replication. Under construction
• Acknowledgements
• Contact us
• Update logs

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Clinical Trials

Section to show on-going clinical trials to figth against COVID-19

U.S. National Library of Medicine, ClinicalTrials.gov, Clinical Trials ordered by treatment

• Anakinra clinical trials
• Azithromycin clinical trials
• Baricitinib clinical trials
• Cobicistat clinical trials
• Colchicina clinical trials
• Darunavir clinical trials
• Hydrychloroquine clinical trials
• Interferon clinical trials
• Lopinavir clinical trials
• Remdesivir clinical trials
• Ritonavir clinical trials
• Sarilumab clinical trials
• Siltuximab clinical trials
• Tocilizumab clinical trials

Clinical Trials in Spain

European Union Clinical Trials Register, Clinical trials for COVID-19

WHO DRAFT landscape of COVID-19 candidate vaccines, now includes two Spanish pre-clinical trials (April 11)

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Educational resources

Harvard Medical School MEDICAL STUDENT COVID-19 CURRICULUM

#AprendeBioinformáticaEnCasa

Bioinformatics Training Resources for Experimentalists (and Friends)

Czech campaign #masks4all We need #masks4all, in Youtube

IAEA International Atomic Energy Agency webinar, COVID-19 and chest CT: protocol and dose optimization

COVID-19 Preparedness for Radiotherapy Departments - Towards Consensus on Best Practices

Actualización sobre la situación de la COVID-19, Dr. Josep Maria Miró

SARS-CoV-2 (COVID-19) by the n. EPIDEMIOLOGY AND GLOBAL HEALTH MICROBIOLOGY AND INFECTIOUS DISEASE elife

International AIDS Society COVID-19 and HIV: Webinar series: "COVID-19 and HIV: What you need to know"

Infectious Disease Modelling: Beyond the Basic SIR Model

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Genomics of SARS-CoV-2

Section devoted to show main findings in the virus genome.

Reproducible analyses for rejecting rare genomic inversions in SARS-CoV-2

SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies

Proyecto Epidemiologia Genomica COVID 19

CovProfile: profiling the viral genome and gene expressions of SARS-COV2

MERS-CoV recombination: implications about the reservoir and potential for adaptation

Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients

The proximal origin of SARS-CoV-2

Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal

Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses

Genomic variations of SARS-CoV-2 suggest multiple outbreak sources of transmission

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing

SARS-CoV-2 Receptor ACE2 is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Enriched in Specific Cell Subsets Across Tissues

RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak

Global patterns in coronavirus diversity

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

LAMP-Seq: Population-Scale COVID-19 Diagnostics Using a Compressed Barcode Space

Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site

The architecture of SARS-CoV-2 transcriptome

Direct RNA sequencing and early evolution of SARS-CoV-2

Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses

Gene expression and in situ protein profiling of candidate SARS-CoV-2 receptors in human airway epithelial cells and lung tissue

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein harbors a conserved BH3-like motif

Knowledge synthesis from 100 million biomedical documents augments the deep expression profiling of coronavirus receptors

In-depth Bioinformatic Analyses of Human SARS-CoV-2, SARS-CoV, MERS-CoV, and Other Nidovirales Suggest Important Roles of Noncanonical Nucleic Acid Structures in Their Lifecycles

Comparative ACE2 variation and primate COVID-19 risk

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Guidelines

A colection of guides and documents from different natianal and international institutions with means to protect people againts COVID-19, including biosafety guidelines, decontamination recommendations and risks, etc. The opinions expressed in there do not reflect ITER institutional position.

WHO - Laboratory Biosafety Manual - Third Edition

SemiSyuc https://semicyuc.org/covid-19/#Documentos Plan de Contingencia para los Servicios de Medicina Intensiva frente a la pandemia COVID-19

Recommended Guidance for Extended Use and Limited Reuse of N95 Filtering Facepiece Respirators in Healthcare Settings

Recomendaciones Institucionales de la Sociedad Española de Enfermedades Infeccionas y Microbiología Clínica (SEIMC)

Documento de posicionamiento de la SEIMC sobre el diagnstico microbiológo de COVID-19

USA CDC Clean & Disinfect Interim Recommendations for US Households with Suspected/Confirmed Coronavirus Disease 2019

WHO Laboratory biosafety guidance related to coronavirus disease (COVID-19) interim guidance, 19 March 2020:

Novel Coronavirus (COVID-19): The American Thoracic Society (ATS) Response

CEN and CENELEC make European standards available to help prevent the COVID-19 contagion

European CDC, Considerations relating to social distancing measures in response to COVID-19 – second update

WHO Home care for patients with COVID-19 presenting with mild symptoms and management of their contacts

WHO several guidelines to protect Workers Health

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Media sources

Selected media articles because of their informative content. The opinions expressed in there do not reflect ITER institutional position.

Financial Times

Example of a device using UV-C for decontamination

Example of a Rapid Bio Decontamination Service, from Bioquell

How did Spain get its coronavirus response so wrong?

Mount Sinai to Begin the Transfer of COVID-19 Antibodies into Critically Ill Patients

Los sesgos que engañan al cerebro durante la pandemia, El País

The Ibuprofen Debate Reveals the Danger of Covid-19 Rumors

Rockefeller-Led Team Launches Initiative to Study COVID-19 Genetic Vulnerability (GenomeWeb)

El Cabildo de Tenerife aporta una máquina de análisis de COVID-19

Investigadores del ITER y de La Candelaria aceleran el método de diagnóstico del Covid-19

COVID-19: Why we should all wear masks — There is new scientific rationale

Over 24,000 coronavirus research papers are now available in one place

How sewage could reveal true scale of coronavirus outbreak

Why It’s So Freaking Hard To Make A Good COVID-19 Model

NYT, Bad News Wrapped in Protein: Inside the Coronavirus Genome

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Protocols

Shared SARS-COV-2 DIAGNOSTIC PIPELINES at FinDX

WHO Coronavirus disease (COVID-19) technical guidance: Laboratory testing for 2019-nCoV in humans (Updated March 25, 2020) In-house developed molecular assays, not validated, probably still under development, but not necessarily updated here

• China CDC Primers and probes for detection 2019-nCoV (24 January 2020)
• Diagnostic detection of Wuhan coronavirus 2019 by real-time RT-PCR – Charité, Berlin Germany (17 January 2020)
• Detection of 2019 novel coronavirus (2019-nCoV) in suspected human cases by RT-PCR – Hong Kong University (23 January 2020)
• PCR and sequencing protocol for 2019-nCoV - Department of Medical Sciences, Ministry of Public Health, Thailand (Updated 28 January 2020)
• PCR and sequencing protocols for 2019-nCoV- National Institute of Infectious Diseases Japan (24 January 2020)
• US CDC Real-Time RT-PCR Panel for Detection 2019-Novel Coronavirus (28 January 2020)
• US CDC panel primer and probes– U.S. CDC, USA (28 January 2020)
• Real-time RT-PCR assays for the detection of SARS-CoV-2 Institut Pasteur, Paris (2 March 2020)

Broad Institute

Analytical sensibility and specificity of two RT-qPCR protocols for SARS-CoV-2 detection performed in an automated workflow

NIID Japan Detection of second case of 2019-nCoV infection in Japan

USA CDC Center for Disease and Control Coronavirus Disease 2019 (COVID-19) RT-PCR protocol

Chinese Center for Disease and Control and Prevention China CDC Real-time RT-PCR protocol

SwabSeq. Allows for detection of SARS-COV-2 genomic RNA, without purification, in a single-step RT-PCR followed by sequencing. By OctanBio

A Massively Parallel COVID-19 Diagnostic Assay for Simultaneous Testing of 19200 Patient Samples, in Twitter | Protocol | Primers & Spike-in Controls

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Rapid Tests

Section to highlight contributions to rapid tests production and testing.

Fast, portable tests come online to curb coronavirus pandemic, Nature. See table inside

COVID-19: immunopathology and its implications for therapy

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Research Coalitions and Funding Calls

Section to collect open calls in the research funding arena.

COVID-19 Clinical Research Coalition

COVID-Zero Coalition

COVID Human Genetic Effort

WHO The Global Preparedness Monitoring Board

CaixaImpulse COVID-19 Call for projects that address the COVID-19 emergency open until 15 April

European Comission Funding & tender opportunities Single Electronic Data Interchange Area (SEDIA)

European Research Council List of ERC-funded Research Projects related to coronavirus

European Comission Coronavirus research and innovation. Research and innovation projects and initiatives to tackle the spread of coronavirus and preparedness for other outbreaks

Solicitud urgente de Expresiones de Interés para la financiacin extraordinaria de proyectos de investigacin sobre el SARS-CoV-2 y la enfermedad COVID-19, Ministerio de Ciencia e Innovacin, España

Fast Funding for COVID-19 Science

The Open COVID Pledge

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Respirators, masks, and other Personal Protective Equipments (PPE)

A selection of websites to understand what a respirator or a mask is, and what are the differences between the different personal protective equipments.

N95 Respirators and Surgical Masks (Face Masks)

Comparison of nanoparticle filtration performance of NIOSH-approved and CE-marked particulate filtering facepiece respirators

Comparison of FFP2, KN95, and N95 and Other Filtering Facepiece Respirator Classes

Ventilators are in high demand for Covid-19 patients. How do they work?

Guías para la fabricación de mascarillas y ropa de protección, Ministerio de Sanidad

Clarificación de los diferentes tipos de mascarillas, Ministerio de Sanidad

Marcado CE de las mascarillas, Ministerio de Industrial, Comercio y Turismo

Widespread use of face masks in public may slow the spread of SARS CoV-2: an ecological study

Face mask use in the general population and optimal resource allocation during the COVID-19 pandemic

Efficacy of face mask in preventing respiratory virus transmission: a systematic review and meta-analysis

Can N95 respirators be reused after disinfection? And for how many times?

N95 Mask Decontamination using Standard Hospital Sterilization Technologies

UV light dosage distribution over irregular respirator surfaces. Methods and implications for safety

Nonmedical Masks in Public for Respiratory Pandemics: Droplet Retention by two-layer Textile Barrier Fully Protects Germ-free Mice from Bacteria in Droplets

Physical interventions to interrupt or reduce the spread of respiratory viruses. Part 1 - Face masks, eye protection and person distancing: systematic review and meta-analysis

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Scientific Communications and Literature (Pre-prints & Peer-Reviewed Papers)

Reminder. Notice that a number of these papers might be preliminary reports that have not been peer-reviewed. They should not be regarded as conclusive, guide clinical practice/health-related behavior, or be reported in news media as established information.

COVID-19 SARS-CoV-2 preprints from medRxiv and bioRxiv

REACTing research & action targeting emerging infectious diseases web portal. Selection of the most relevant articles published on COVID-19 on a bi-weekly basis. France

SemanticScholar COVID-19 Open Research Dataset (CORD-19)

Early warnings of novel coronavirus from genomic epidemiology and the global open scientific response

A Novel Coronavirus from Patients with Pneumonia in China, 2019

Novel 2019 coronavirus genome

Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia

Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1

A pneumonia outbreak associated with a new coronavirus of probable bat origin

Research and Development on Therapeutic Agents and Vaccines for COVID-19 and Related Human Coronavirus Diseases

A new coronavirus associated with human respiratory disease in China

Rational use of face masks in the COVID-19 pandemic

Three Emerging Coronaviruses in Two Decades The Story of SARS, MERS, and Now COVID-19

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

Characteristics of pediatric SARS-CoV-2 infection and potential evidence for persistent fecal viral shedding

A contingency plan for the management of the 2019 novel coronavirus outbreak in neonatal intensive care units

Managing neonates with respiratory failure due to SARS-CoV-2

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study

Clinical Features of 69 Cases with Coronavirus Disease 2019 in Wuhan,China

Coronavirus Disease 2019: Coronaviruses and Blood Safety

COVID-19: what is next for public health?

Transmission of 2019-nCoV Infection from an Asymptomatic Contact in Germany

Understanding of COVID-19 based on current evidence

Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1

Clinical Characteristics of Coronavirus Disease 2019 in China

A Trial of Lopinavir–Ritonavir in Adults Hospitalized with Severe Covid-19

CDC Coronavirus Disease 2019 (COVID-19) publications

Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia

NIID National Institute for Infectious Diseases Manual for the Detection of Pathogen 2019-nCoV

Coronavirus Disease 2019 (COVID-19) in Italy

Case-Fatality Rate and Characteristics of Patients Dying in Relation to COVID-19 in Italy

Critical Care Utilization for the COVID-19 Outbreak in Lombardy, Italy. Early Experience and Forecast During an Emergency Response

Detection of SARS-CoV-2 in Different Types of Clinical Specimens

OVID-19 in Singapore—Current Experience: Critical Global Issues That Require Attention and Action

Coronavirus Disease 2019 and Influenza

Coronavirus Infections—More Than Just the Common Cold

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis

Diagnosis of Acute Respiratory Syndrome Coronavirus 2 Infection by Detection of Nucleocapsid Protein

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study

Transcriptional Inhibition of Host Viral Entry Proteins as a Therapeutic Strategy for SARS-CoV-2

Human leukocyte antigen susceptibility map for SARS-CoV-2

An international comparison of the second derivative of COVID-19 deaths after implementation of social distancing measures

Estimating the number of infections and the impact of nonpharmaceutical interventions on COVID-19 in 11 European countries

Susceptibility of ferrets, cats, dogs, and different domestic animals to SARS-coronavirus-2

Clinical and virological data of the first cases of COVID-19 in Europe: a case series

SARS-CoV-2 detection from nasopharyngeal swab samples without RNA extraction

Nature Special Report. Special report: The simulations driving the world’s response to COVID-19. How epidemiologists rushed to model the coronavirus pandemic

Respiratory virus shedding in exhaled breath and efficacy of face masks

SARS-CoV-2 neutralizing serum antibodies in cats: a serological investigation

Virological assessment of hospitalized patients with COVID-2019

Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins

Potent Antiviral Activities of Type I Interferons to SARS-CoV-2 Infection

Chest CT for Typical 2019-nCoV Pneumonia: Relationship to Negative RT-PCR Testing

Is low dose radiation therapy a potential treatment for COVID-19 pneumonia?

Clinical characteristics of the recovered COVID-19 patients with re-detectable positive RNA test

The convalescent sera option for containing COVID-19

Novel Coronavirus Infection in Newborn Babies Under 28 Days in China

A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests

Loss of smell and taste in combination with other symptoms is a strong predictor of COVID-19 infection

Toilets dominate environmental detection of SARS-CoV-2 virus in a hospital

Validation of a Lysis Buffer Containing 4 M Guanidinium Thiocyanate (GITC)/ Triton X-100 for Extraction of SARS-CoV-2 RNA for COVID-19 Testing: Comparison of Formulated Lysis Buffers Containing 4 to 6 M GITC, Roche External Lysis Buffer and Qiagen RTL Lysis Buffer

An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 in human airway epithelial cell cultures and multiple coronaviruses in mice

Estimation of the percentages of asymptomatic patients and undiagnosed patients of the novel coronavirus (SARS-CoV-2) infection in Hokkaido, Japan by using birth-death process with recursive full tracing

Blueprint for a Pop-up SARS-CoV-2 Testing Lab

Cutaneous manifestations in COVID‐19: a first perspective

Dermatology staff participate in fight against Covid-19 in China

Severe Acute Respiratory Syndrome Coronavirus 2 RNA Detected in Blood Donations

Structural Basis for the Inhibition of the RNA-Dependent RNA Polymerase from SARS-CoV-2 by Remdesivir

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Maths and Epidemiological Models

Subsection dedicated to PCR (RT-qPCR) and related topics.

Modelo para el estudio de la dinámica de transmisión del SARS-CoV-2 y la enfermedad COVID19. Descripción técnica

The use of facemasks to prevent respiratory infection: a literature review in the context of the Health Belief Model

Reproductive numbers, epidemic spread and control in a community of households

Mathematical Modeling of the Effectiveness of Facemasks in Reducing the Spread of Novel Influenza A (H1N1)

The role of facemasks and hand hygiene in the prevention of influenza transmission in households: results from a cluster randomised trial; Berlin, Germany, 2009-2011

Mask use, hand hygiene, and seasonal influenza-like illness among young adults: A randomized intervention trial

Unraveling R0: Considerations for Public Health Applications

The Immediate Effect of COVID-19 Policies on Social Distancing Behavior in the United States

Flattening the curve before it flattens us: hospital critical care capacity limits and mortality from novel coronavirus (SARS-CoV2) cases in US counties - 3 and 6 week projections from April 2, 2020

Sustainable social distancing through facemask use and testing during the Covid-19 pandemic

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PCR related articles and other detection techniques

Subsection dedicated to PCR (RT-qPCR) and related topics.

Combination of RT‐qPCR testing and clinical features for diagnosis of COVID‐19 facilitates management of SARS‐CoV‐2 outbreak

Positive RT-PCR Test Results in Patients Recovered From COVID-19

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swab using Qiagen RNEasy kits or directly via omission of an extraction step

DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP

Analytical sensibility and specificity of two RT-qPCR protocols for SARS-CoV-2 detection performed in an automated workflow

Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-Co2 virus detection

Reverse-transcription quantitative PCR directly from cells without RNA extraction and without isothermal reverse-transcription: a ‘zero-step’ RT-qPCR protocol

Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR

Efficient and Practical Sample Pooling High-Throughput PCR Diagnosis of COVID-19

The Potential Use of Unprocessed Sample for RT-qPCR Detection of COVID-19 without an RNA Extraction Step

Optimization of SARS-CoV-2 detection by RT-QPCR without RNA extraction

Variation in False Negative Rate of RT-PCR Based SARS-CoV-2 Tests by Time Since Exposure

Report from the American Society for Microbiology COVID-19 International Summit, 23 March 2020: Value of Diagnostic Testing for SARS–CoV-2/COVID-19

Rapid colorimetric detection of COVID-19 coronavirus using a reverse tran-scriptional loop-mediated isothermal amplification (RT-LAMP) diagnostic plat-form: iLACO

Non-specific Primers Reveal False-negative Risk in Detection of COVID-19 Infections

Fast SARS-CoV-2 detection by RT-qPCR in preheated nasopharyngeal swab samples

Development of a Laboratory-safe and Low-cost Detection Protocol for SARS-CoV-2 of the Coronavirus Disease 2019 (COVID-19)

An alternative workflow for molecular detection of SARS-CoV-2 - escape from the NA extraction kit-shortage

High-throughput extraction of SARS-CoV-2 RNA from nasopharyngeal swabs using solid-phase reverse immobilization beads

A streamlined approach to rapidly detect SARS-CoV-2 infection, avoiding RNA extraction

SARS-CoV-2 detection with CRISPR diagnostics

Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP

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Scientific Data and Resources

2019 Novel Coronavirus COVID-19 (2019-nCoV) Data Repository by Johns Hopkins CSSE

Nextstrain. Real-time tracking of pathogen evolution

Artic Network

GISAID

NCBI SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequences

Virological

National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences Released genomes

EMBL-EBI COVID-19 Portal

Coronavirus Structural Task Force

SWISSMODEL homology models

Nanopore (ONT) Novel Coronavirus information(COVID-19)

Clustering COVID-19 research papers

Análisis de los datos de COVID-19 en España, por Z Data Labs

COVID-19 3D visualizer

Coronavirus COVID-19 Global Cases by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU)

Uniform analysis of coronavirus and SARS-COV-2 nanopore direct RNA sequencing datasets using MasterOfPores

European Centre for Disease Prevention and Control European Centre for Disease Prevention and Control, data

European Data Portal, data for Spain, Evolución de enfermedad por el coronavirus (COVID-19)

IHME, Institute for Health Metrics and Evaluation, USA data

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Ministerio de Sanidad, España

Informes MoMo (Sistema de Monitorización de la Mortalidad Diaria (Sistema MoMo) del Instituto de Salud Carlos III

Instituto de Matemática Interdisciplinar de la Universitat Politécnica de Valencia (UPV) Modelling Uncertainty Quantification, Reports in PDF Modelización epidemiolgica: Informes

Bioinformatics Unit of Instituto de Salud Carlos III (Spain)

SARS-CoV-2 Galaxy Project

COVID-19 scenarios

Imperial College London reports

COVID-19: on average only 6% of actual SARS-CoV-2 infections detected worldwide, University of Göttingen

NIH Coronavirus Disease 2019 Situation Summary

Bioinformatics resources for SARS-CoV-2

Coronavirus analysis tools developed by scientists at the University of Tartu, Estonia

SARS-CoV-2 Sequencing Resources

COVID-19 Open Research Dataset Challenge (CORD-19)

World-o-Meter

How many tests for COVID-19 are being performed around the world?

Epidemic Calculator

SARS-CoV-2 pathways

Evolución del coronavirus (COVID-19) en Euskadi

CDC Morbidity and Mortality Weekly Report (MMWR) Novel Coronavirus Reports

COVID-19 R-shiny codes

CDC Information for Laboratories RT-PCR resources

COVID-19 Tracker Shiny app in R

United Against COVID-19

PolyMath COVID-19 dataset clearinghouse

Discourse Data Against Covid19

DataStudio International-Domestic spreading of 2019-nCoV-V4

CSVS Babelomics Collaborative Spanish Variant Server to visualize polimorphisms in the Spanish population in genes related with COVIDー19

Jupyter R notebook for prediction modelling of Covid-19 data. Predictive modelling of 2019-nCov outbreak data in Canary Islands. Departamento de Matemáticas, Estadística e Investigación Operativa, ULL

Explore the Spread of Covid-19, Humboldt-Universität zu Berlin

COVID-19 Host Genetics Initiative

The COVID Tracking Project, testing data available for US states and territories

ETE team modeling group ( MIVEGEC Laboratory , CNRS, IRD, University of Montpellier)

MIDAS 2019 Novel Coronavirus Repository

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List of institutional websites for the governments of each of the Spanish Autonomous Regions (17) and Cities (2).

Autonomous Regions and Cities in Spain:

• Aragón
• Principado de Asturias
• Castilla La Mancha Datos
• Portal del GOBCAN con el seguimiento de la pandemia por SARS-Cov-2 Canarias. Informes epidemiológicos de Salud Pública de la Consejería de Sanidad del Gobierno Autónomo de Canarias
• Generalitat de Catalunya Datos
• Cantabria
• Ciudad Autónoma de Ceuta
• Govern Illes Balears
• Junta de Andalucía
• Junta de Extremadura
• Xunta de Galicia
• Junta de Castilla y León. Situación epidemiológica del coronavirus en Castilla y León — Análisis de datos abiertos JCyL
• Madrid | Covid 19 -TIA Zonas Básicas de Salud - Conjuntos de datos - Datos Abiertos Comunidad de Madrid
• Ciudad Autónoma de Melilla
• Navarra Datos
• País Vasco
• Región de Murcia
• La Rioja
• Generalitat Valenciana

Casos de Covid-19 en España por Comunidades Autónomas, by CJP

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Sequencing, Sequences and Bioinformatics

Under construction. Soon here!

NCBI GenBank SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequences

NCBI GenBank Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome. GenBank: MN908947.3

China National Center for Bioinformation (CNCB), 2019 Novel Coronavirus Resource | Genome Variation | Data release statistics

Centre for Genomic Regulation, CRG, public.docs repository, COVID sequences, including fast5 files

COVID-19 ARTIC v3 Illumina library construction and sequencing protocol

Enrichment workflow for detecting coronavirus using Illumina NGS systems

CDC GitHub SARS-CoV-2 Sequencing Resources

Katarina Braun GitHub ARS-CoV-2_sequencing repository

Broad Institute viral-related pipelines. Several available repositories with scripts and tools for the analysis of viral NGS data

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Shiny and R related dashboards and packages

Section to show relevant Shiny dashborads, R packages and codes. Under construction...

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Viral mechanisms and Tropism: infection, entry, and replication

Section to describe the different mechanisms and tropism that the virus displays. Under construction...

Immunoglobulin fragment F(ab')2 against RBD potently neutralizes SARS-CoV-2 in vitro

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Acknowledgements

Section to highlight the contributors of many links within this repository. Want to share your relevant links? Place a Direct Message to @resocios in Twitter.

• Agustín Valenzuela Fernández (ULL) @SciArt3
• Carlos Javier Pérez González (ULL) @cpgonzal
• José Luis Roda (ULL) @joluroga
• Marcos Colebrook Santamaría (ULL) @MColebrook
• María López Pérez (FIMERALL-SEGAI, ULL)
• Carlos Flores Infante (FIISC, ITER) @LabCflores

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Contact us

Want to contact us? Please, send me a Direct Message on Twitter (see below).

Last update: 23:21 GMT - April 13, 2020 | By JMLS @resocios

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Update logs

April 12, 2020 updates: new articles regarding COVID-19 detection, a comprehensive draft list of clinical trials by country from WHO (update April 11), dermatological effects of COVID-19, a new report from University of Göttingen, and many more.

April 11, 2020 updates: new rapid PCR methods to detect COVID-19; warning about the use on non-specific PCR primers and False Negatives; more on the disinfection of respirators.

April 10, 2020 updates: new logos; new papers in Scientic Literature; new subsection "Maths and Epidemiological Models", where the impact of social distancing and face mask use are presented.

April 9, 2020 updates: new entries in the scientific literature section (PCR false negatives and COVID-19 affecting newborn babies, among others); new entry in the genomics section; new subsection dedicated to PCR and related topics within the Scientific Literature section; new articles related to respiratory protective equipment and ways to disinfect them; new section about sequencing and sequences.