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COVID-19

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

August 12, 2020 updates. Two new sections on Government COVID 19 Contingency Plans for Schools Reopening and Emerging Disease Challenges, together with a bunch of additional resources: airborne transmission (3); saliva based testing (1); schools (and other human-populated spaces) reopenings (5); epidemiology (4); media sources (3); pooling and group testing (1); PCR related methods (3); research coalitions and funding calls (1); seroprevalence (1); sequencing (4)... Enjoy the reading! ;=)

As the repository has largely increased its size, it is also available in WIKI format here for your convenience.

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

Table of contents

Apps for COVID tracking

New section on July 4, 2020.

Apple and Google’s covid-tracing tech has been released to 23 countries

Balancing functionality with Privacy for Effective Contact Tracing Apps

BlueTrace: A privacy-preserving protocol for community-driven contact tracing across borders

Coronavirus contact-tracing apps: can they slow the spread of COVID-19?

Digital contact tracing: comparing the capabilities of centralised and decentralised data architectures to effectively suppress the COVID-19 epidemic whilst maximising freedom of movement and maintaining privacy

DP3T - Decentralized Privacy-Preserving Proximity Tracing

Effective configurations of a digital contact tracing app: A report to NHSX

Haz tu autoevaluación del COVID-19, Ministerio de Sanidad

It is possible to stop the epidemic

Pan-European Privacy-Preserving Proximity Tracing

Airborne transmission

New section on August 3, 2020.

A Letter about the Airborne Transmission of SARS-CoV-2 Based on the Current Evidence

Aerosol and surface contamination of SARS-CoV-2 observed in quarantine and isolation care

Airborne Transmission of SARS-CoV-2 Theoretical Considerations and Available Evidence

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

Aerosol transmission of SARS-CoV-2. Evidence for probable aerosol transmission of SARS-CoV-2 in a poorly ventilated restaurant

Airborne Spread of SARS-CoV-2 and a Potential Role for Air Disinfection

Airborne Transmission of COVID-19: Epidemiologic Evidence from An Outbreak Investigation

Airborne transmission of SARS-CoV-2: The world should face the reality

Airborne Transmission Route of COVID-19: Why 2 Meters/6 Feet of Inter-Personal Distance Could Not Be Enough

Arguments pour une possible transmission par voie aérienne du SARS-CoV-2 dans la crise COVID-19. Evidences for a possible airborne transmission of SARS-CoV-2 in the COVID-19 crisis

Choir practice turns fatal. Coronavirus is to blame

Covid-19: Airborne transmission is being underestimated, warn experts

Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients

Detection of Airborne Severe Acute Respiratory Syndrome (SARS) Coronavirus and Environmental Contamination in SARS Outbreak Units

Droplets and Aerosols in the Transmission of SARS-CoV-2

How can airborne transmission of COVID-19 indoors be minimised?

Identifying airborne transmission as the dominant route for the spread of COVID-19

If the coronavirus is really airborne, we might be fighting it the wrong way

Indoor transmission of SARS-CoV-2

Intense fitness classes can lead to rapid spread of COVID-19, report shows

Japan's supercomputer suggests changes to travel, work amid airborne virus threat

Mounting evidence suggests coronavirus is airborne — but health advice has not caught up

Respiratory Transmission of SARS-CoV-2: What Do We Really Know?

Respiratory virus shedding in exhaled breath and efficacy of face masks

Role of air distribution in SARS transmission during the largest nosocomial outbreak in Hong Kong

SARS-CoV-2 failure to infect or replicate in mosquitoes: an extreme challenge

Severe COVID-19 in the young and healthy: monogenic inborn errors of immunity?

Transmission of SARS-CoV-2: implications for infection prevention precautions

Viable SARS-CoV-2 in the air of a hospital room with COVID-19 patients

We Need to Talk About Ventilation

Book chapters

New section on May 2, 2020.

Coronaviruses, Chapter 31, Fenner and White's Medical Virology (Fifth Edition (Elsevier's Academic Press, 2017)

Coronaviruses, Including Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS), Chapter 155, Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, Ninth Edition (Elsevier, 2020)

Disaster Epidemiology and Surveillance, Chapter 27, Jekel's Epidemiology, Biostatistics, Preventive Medicine, and Public Health, 5th Edition (Elsevier, 2020)

Novel Coronavirus from Wuhan China, 2019-20, Update to Chapter 155, Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, Ninth Edition (Elsevier, 2020)

Viral Infections, Chapter 32, Murray and Nadel’s Textbook of Respiratory Medicine, Sixth Edition (Elsevier, 2016)

Clinical Trials and Pharmacological Treatments

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

Clinical Trials in Spain

Pharmacologic Treatments for Coronavirus Disease 2019 (COVID-19). A review

Recent progress and challenges in drug development against COVID-19 coronavirus (SARS-CoV-2) - an update on the status

STAT's Covid-19 Drugs and Vaccines Tracker

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

Clinics

New section on May 16, 2020.

A Randomized Trial of Hydroxychloroquine as Postexposure Prophylaxis for Covid-19

Age Matters: COVID-19 Prevalence in a Vaping Adolescent Population - An Observational Study

Air Hunger and Psychological Trauma in Ventilated COVID-19 Patients: An Urgent Problem

Airway expression of SARS-CoV-2 receptor, ACE2, and proteases, TMPRSS2 and furin, in severe asthma

An outbreak of severe Kawasaki-like disease at the Italian epicentre of the SARS-CoV-2 epidemic: an observational cohort study

Are COVID-19 Patients Dying of or with Cardiac Injury?

Autopsy Findings and Venous Thromboembolism in Patients With COVID-19: A Prospective Cohort Study

Bacterial and fungal co-infection in individuals with coronavirus: A rapid review to support COVID-19 antimicrobial prescribing

Characterization of the Inflammatory Response to Severe COVID-19 Illness

Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections

Clinical Characteristics and Results of Semen Tests Among Men With Coronavirus Disease 2019

Clinical classifiers of COVID-19 infection from novel ultra-high-throughput proteomics

Clinical importance of reporting SARS-CoV-2 viral loads across the different stages of the COVID-19 pandemic

Clinical Utility of SARS-CoV-2 Whole Genome Sequencing in Deciphering Source of Infection

Coinfections in COVID-19

Coughs and Sneezes: Their Role in Transmission of Respiratory Viral Infections, Including SARS-CoV-2

Covert COVID-19 and false-positive dengue serology in Singapore

COVID-19 Autopsies, Oklahoma, USA

COVID-19 Lung Injury and “Typical” ARDS: The Danger of Presumed Equivalency

COVID-19 Phenotypes and Potential Harm of Conventional Treatments: How to Prove the Hypothesis

COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis

Critically ill SARS-CoV-2 patients display lupus-like hallmarks of extrafollicular B cell activation

Culture-Competent SARS-CoV-2 in Nasopharynx of Symptomatic Neonates, Children, and Adolescents

Description of COVID-19 in HIV-infected individuals: a single-centre, prospective cohort

Dengue antibodies can cross-react with SARS-CoV-2 and vice versa-Antibody detection kits can give false-positive results for both viruses in regions where both COVID-19 and Dengue co-exist

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

Evolution and epidemic spread of SARS-CoV-2 in Brazil

Expression of the SARS-CoV-2 ACE2 Receptor in the Human Airway Epithelium

Extracorporeal Membrane Oxygenation for Critically Ill Patients with COVID-19 Related Acute Respiratory Distress Syndrome: Worth the Effort?

Heterogeneity of Acute Respiratory Distress Syndrome in COVID-19: “Typical” or Not?

IL6 inhibition in critically ill COVID-19 patients is associated with increased secondary infections

Mechanics of Breathing and Gas Exchange in Mechanically Ventilated Patients with COVID-19 Associated Respiratory Failure

Outbreak of Kawasaki disease in children during COVID-19 pandemic: a prospective observational study in Paris, France

Pathological findings of COVID-19 associated with acute respiratory distress syndrome

Possible use of the mucolytic drug, bromhexine hydrochloride, as a prophylactic agent against SARS-CoV-2 infection based on its action on the Transmembrane Serine Protease 2

Prior infection by seasonal coronaviruses does not prevent SARS-CoV-2 infection and associated Multisystem Inflammatory Syndrome in children

Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period

Reply to: Are COVID-19 Patients Dying of or with Cardiac Injury?

Respiratory Mechanics and Gas Exchange in COVID-19 Associated Respiratory Failure

RETRACTED: Hydroxychloroquine or chloroquine with or without a macrolide for treatment of COVID-19: a multinational registry analysis

SARS-CoV-2 viral load in the upper respiratory tract of children and adults with early acute COVID-19

Severe Hypoxemia in Early COVID-19 Pneumonia

Shared SARS-CoV-2 diversity suggests localised transmission of minority variants

Standards and Stereotypes in COVID-19

Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV-2)

Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo’

Telemedicine-Enabled Accelerated Discharge of Hospitalized COVID-19 Patients to Isolation in Repurposed Hotel Rooms

The COVID-19 Pandemic Presents an Opportunity to Reassess the Value of Polysomnography

The hallmarks of COVID-19 disease

Tobacco Smoking Increases the Lung Gene Expression of ACE2, the Receptor of SARS-CoV-2

Treatment of COVID-19 by Inhaled NO to Reduce Shunt?

Understanding pathophysiology of hemostasis disorders in critically ill patients with COVID‑19

Unravelling the debate on heme effects in COVID-19 infections

Ventilator Sharing During an Acute Shortage Caused by the COVID-19 Pandemic

Viable SARS-CoV-2 in various specimens from COVID-19 patients

Diagnostics

New section on April 26, 2020.

A case of a readmitted patient who recovered from COVID-19 in Chengdu, China

Chest CT findings of COVID-19 pneumonia by duration of symptoms

Coagulation disorders in coronavirus infected patients: COVID-19, SARS-CoV-1, MERS-CoV and lessons from the past

Coronavirus Standards Working Group. A COVID-19 Diagnostic Standards Development Partnership

COVID-19 diagnosis and study of serum SARS-CoV-2 specific IgA, IgM and IgG by a quantitative and sensitive immunoassay

Critically ill SARS-CoV-2 patients display lupus-like hallmarks of extrafollicular B cell activation

Diagnosis of the Coronavirus disease (COVID-19): rRT-PCR or CT?

Distinguishing COVID-19 from influenza pneumonia in the early stage through CT imaging and clinical features

Development of Reverse Transcription Loop-Mediated Isothermal Amplification Assays Targeting SARS-CoV-2

Evaluation of coronavirus in tears and conjunctival secretions of patients with SARS‐CoV‐2 infection

Failed detection of the full-length genome of SARS-CoV-2 by ultra-deep sequencing from the recovered and discharged patients retested viral PCR positive

Imaging of coronavirus disease 2019: A Chinese expert consensus statement. Review

Interpreting a covid-19 test result

PCR Assays Turned Positive in 25 Discharged COVID-19 Patients

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

Positive RT-PCR tests among discharged COVID-19 patients in Shenzhen, China

Predictive value of sudden olfactory loss in the diagnosis of COVID-19

Presymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing Facility

Rates of Co-infection Between SARS-CoV-2 and Other Respiratory Pathogens

SARS-CoV-2-Positive Sputum and Feces After Conversion of Pharyngeal Samples in Patients With COVID-19

SARS-CoV-2 Infection in Children

SARS-CoV-2 turned positive in a discharged patient with COVID-19 arouses concern regarding the present standard for discharge

Serial CT features in discharged COVID-19 patients with positive RT-PCR re-test

Seven discharged patients turning positive again for SARS-CoV-2 on quantitative RT-PCR

Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction–Based SARS-CoV-2 Tests by Time Since Exposure

Educational resources

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

#AprendeBioinformáticaEnCasa

Así es la lucha entre el sistema inmune y el coronavirus. El País

Bioinformatics Training Resources for Experimentalists (and Friends)

CommonCraft COVID Communication Kit

COVID-19 Contact Tracing

COVID-19 Immunology 101 for Non-immunologists by Akiko Iwasaki, Ph.D.

COVID19: Top 7 online interactive simulations, curated

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

Czech campaign #masks4all We need #masks4all, in Youtube

Harvard Medical School MEDICAL STUDENT COVID-19 CURRICULUM

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

Infectious Disease Modelling: Beyond the Basic SIR Model

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

Interpreting a covid-19 test result

Learning Without Borders: Asynchronous and Distance Learning in the Age of COVID-19 and Beyond

Los virus más infecciosos del último siglo, en imágenes, diario El País, España

¿Qué pasará ahora? Los futuros de la COVID-19 explicados con simulaciones

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

The race for coronavirus vaccines: a graphical guide

The woman who discovered the first coronavirus

Emerging Diseases Challenges

PRESENTACIÓN DEL INFORME RETOS ENFERMEDADES INFECCIOSAS - CIENCIA EN EL PARLAMENTO DE CANARIAS, título "Respuestas a las evidencias solicitadas sobre los retos que nos plantean las enfermedades infecciosas". Published on Apr 12, 2020; por @SciArt3D, Lab Inmunología Celular y Viral, ULL, para el Parlamento sobre el Reto, Amenazas y Oportunidades de desarrollo que suponen las Enfermedades Infecciones, como las últimamente frecuentes por Virus Emergentes

PRESENTACIÓN DEL INFORME RETOS ENF. INFECCIOSAS - COLOQUIO CIENCIA EN EL PARLAMENTO ULL (11-X-2019). Published on Apr 13, 2020; por @SciArt3D, Lab Inmunología Celular y Viral, ULL, Mesa Coloquio sobre las amenazas, retos y oportunidades asociadas a las grandes pandemias por enfermedades emergentes. Focalizando en virus emergentes en el s. XXI por globalización, turismo de masas (Islas Canarias y sector turístico como vector y en riesgo como sector económico), comercio internacional con países líder como China (vector de propagación y partner obligado de cooperación)

Epidemiology

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

A “One-Health” approach for diagnosis and molecular characterization of SARS-CoV-2 in Italy

‘All In’: A Pragmatic Framework for COVID-19 Testing and Action on a Global Scale

Airborne Transmission of COVID-19: Epidemiologic Evidence from An Outbreak Investigation

Analysis of the impact of lockdown on the evolution Covid-19 epidemics in Spain

Analysis of the time evolution of SARS-CoV-2 lethality rate in Italy: Evidence of an unaltered virus potency

Asymptomatic Transmission, the Achilles’ Heel of Current Strategies to Control Covid-19

BCG VACCINES MAY NOT REDUCE COVID-19 MORTALITY RATES

Changes in contact patterns shape the dynamics of the COVID-19 outbreak in China

Considering how biological sex impacts immune responses and COVID-19 outcomes

Coronavirus Disease Outbreak in Call Center, South Korea

COVID-19 Asymptomatic Infection Estimation

COVID-19 and Postinfection Immunity Limited Evidence, Many Remaining Questions

COVID-19 Disease Dynamics in Germany: First Models and Parameter Identification

COVID-19 Outbreak Associated with Air Conditioning in Restaurant, Guangzhou, China, 2020

Data-driven estimation of change points reveal correlation between face mask use and accelerated curtailing of the COVID-19 epidemic in Italy

Detection of SARS-CoV-2 RNA on public surfaces in a densely populated urban area of Brazil

Early detection of superspreaders by mass group pool testing can mitigate COVID-19 pandemic

Estimating the burden of SARS-CoV-2 in France

Estimating the probability of New Zealand regions being free from COVID-19 using a stochastic SEIR model

Estimation of SARS-CoV-2 emissions from non-symptomatic cases

Estimates of the ongoing need for social distancing and control measures post-"lockdown" from trajectories of COVID-19 cases and mortality

Evidence for probable aerosol transmission of SARS-CoV-2 in a poorly ventilated restaurant

Evolving Epidemiology and Impact of Non-pharmaceutical Interventions on the Outbreak of Coronavirus Disease 2019 in Wuhan, China

First detection of SARS-CoV-2 in untreated wastewaters in Italy

Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California

How did SARS-CoV-19 spread in India from Italy, Iran and China? Genetic surveillance of early cases and virus demography

How the pandemic might play out in 2021 and beyond

Identifying airborne transmission as the dominant route for the spread of COVID-19

INTRODUCTIONS ET CIRCULATION INITIALE DU SARS-COV-2 EN FRANCE

Modeling infectious epidemics

Natural History of Asymptomatic SARS-CoV-2 Infection

Outbreak dynamics of COVID-19 in Europe and the effect of travel restrictions

Presymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing Facility

Public Health Interventions for COVID-19: Emerging Evidence and Implications for an Evolving Public Health Crisis. JAMA editorial | Infectious Diseases

Relationship between COVID-19 death toll doubling time and national BCG vaccination policy

Scientists are drowning in COVID-19 papers. Can new tools keep them afloat?

Susceptibility to and transmission of COVID-19 amongst children and adolescents compared with adults: a systematic review and meta-analysis

Strategies to reduce the risk of SARS-CoV-2 re-introduction from international travellers

Successful Elimination of Covid-19 Transmission in New Zealand | New Zealand orders lockdown after four new COVID-19 cases emerge

Sustained suppression

Temporal variation in transmission during the COVID-19 outbreak

The fate of house cats during the COVID-19 pandemic

The PHA4GE SARS-CoV-2 Contextual Data Specification for Open Genomic Epidemiology

The incubation period of COVID-19: A rapid systematic review and meta-analysis of observational research

Why does COVID-19 case fatality rate vary among countries?

Genomics and Phylodynamics of SARS-CoV-2

Section devoted to show main findings in the virus genome.

A Computational Toolset for Rapid Identification of SARS-CoV-2, other Viruses, and Microorganisms from Sequencing Data

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

An 81 base-pair deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020)

A New Resource for Genomics and Precision Health Information and Publications on the Investigation and Control of COVID-19 and other Coronaviruses

Characterization of intra-host SARS-CoV-2 variants improves phylogenomics reconstruction and may reveal functionally convergent mutations

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

Comparative ACE2 variation and primate COVID-19 risk

Comparative transcriptome analysis reveals the intensive early-stage responses of host cells to SARS-CoV-2 infection

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

CoV-GLUE. Virus genome analysis for the SARS-CoV-2 pandemic

COVID-19 Cell Atlas

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

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

Elevated Plasmin(ogen) as a Common Risk Factor for COVID-19 Susceptibility

Emergence of genomic diversity and recurrent mutations in SARS-CoV-2

Emergence of multiple variants of SARS-CoV-2 with signature structural changes

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

Failed detection of the full-length genome of SARS-CoV-2 by ultra-deep sequencing from the recovered and discharged patients retested viral PCR positive

Genomewide Association Study of Severe Covid-19 with Respiratory Failure

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

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

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

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

Global patterns in coronavirus diversity

How fast does the SARS-Cov-2 virus really mutate in heterogeneous populations?

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

Issues with SARS-CoV-2 sequencing data

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

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

Massive Multiplexing Can Deliver a $1 Test for COVID-19

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

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

Phylodynamics of SARS-CoV-2 transmission in Spain

Presence of Genetic Variants Among Young Men With Severe COVID-19

Proyecto Epidemiologia Genomica COVID 19

Proyecto SeqCOVID – Genomic epidemiology of SARS-CoV-2 in Spain

Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections

Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform

Revealing variants in SARS-CoV-2 interaction domain of ACE2 and loss of function intolerance through analysis of >200,000 exomes

Quality control of low-frequency variants in SARS-CoV-2 genomes

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

REVEALING COVID-19 TRANSMISSION BY SARS-CoV-2 GENOME SEQUENCING AND AGENT BASED MODELLING

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

SARS coronavirus 2 in Viral Zone / Covid-19 genome expression

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

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

Sequence Characterization and Molecular Modeling of Clinically Relevant Variants of the SARS-CoV-2 Main Protease

Specific mutations in SARS-CoV2 RNA dependent RNA polymerase and helicase alter protein structure, dynamics and thus function: Effect on viral RNA replication

Synonymous mutations and the molecular evolution of SARS-Cov-2 origins

The architecture of SARS-CoV-2 transcriptome

The genomic variation landscape of globally-circulating clades of SARS-CoV-2 defines a genetic barcoding scheme

The proximal origin of SARS-CoV-2

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

ViralZone. SARS coronavirus 2 / Covid-19 genome expression

Guidelines, Society's Clinical and Professional Statements, and Reports

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

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

Coronavirus Standards Working Group. A COVID-19 Diagnostic Standards Development Partnership

Documento de posicionamiento de la SEIMC sobre el diagnóstico microbiológico de COVID-19

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

Fichas InfoSEV de la Sociedad Española de Virología con información básica para dar respuesta a las preguntas más frecuentes sobre el coronavirus SARS-CoV-2 y la enfermedad COVID-19

How COVID-19 is changing the world: a statistical perspective

Interim Guidelines for Clinical Specimens for COVID-19 | CDC

Interim Guidance for Use of Pooling Procedures in SARS-CoV-2 Diagnostic, Screening, and Surveillance Testing

Interim Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with Coronavirus Disease 2019 (COVID-19)

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

NIH COVID-19 Treatment Guidelines

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)

SEI Sociedad Española de Inmunología: test de detección de anticuerpos, pruebas de anticuerpos anti SARS-CoV-2 y diagnóstico de infección por SARS-CoV-2

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

SemiSyuc | Plan de Contingencia para los Servicios de Medicina Intensiva frente a la pandemia COVID-19

Transmission of SARS-CoV-2: implications for infection prevention precautions

Weekly Coronavirus Disease 2019 (COVID-19) Surveillance Report Summary of COVID-19 surveillance systems

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

WHO several guidelines to protect Workers Health

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

WHO - Laboratory Biosafety Manual - Third Edition

Government COVID 19 Contingency Plans for Schools Reopening

Section linking the official government contingency plans for the reopenings of non-universitary schools per region in Spain in 2020-2021

MINISTERIO DE EDUCACIÓN Y FORMACIÓN PROFESIONAL

Medidas COVID-19

ANDALUCIA

Portal web de la Consejería de Educación y Deporte

Decálogo para una vuelta segura a la actividad educativa presencial y respuestas a todas las consultas, dudas y cuestiones que las direcciones de los centros, y los docentes en general, han planteado hasta la fecha

Instrucción 10/2020, de 15 de junio, sobre las medidas educativas a adoptar en el incio del curso 2020/2021 en los centros docentes andaluces que imparten enseñanzas de régimen general

ARAGÓN

Portal web del Departamento de Educación, Cultura y Deporte

Procedimiento de actuación y otras informaciones frente a casos de infección por el nuevo coronavirus en Aragón (COVID-19)

PRINCIPADO DE ASTURIAS

Portal web de la Consejería de Educación

Resolución reanudación presencial de las clases en el curso escolar 2020-2021. Plan de Contingencia

ILLES BALEARS

Portal web de la Consejería de Educación, Universidad e Investigación

Orientacions per a l'elaboració del pla de contingència

CANARIAS

Portal web de la Consejería de Educación, Universidades, Cultura y Deportes

Protocolo de prevención y organización para el desarrollo de la actividad educativa presencial en los centros educativos no universitarios de Canarias. Curso académico 2020-2021

CANTABRIA

Portal web de la Consejería de Educación, Formación Profesional y Turismo

Protocolos de prevención COVID-19

CASTILLA Y LEON

Portal web de Educación

Protocolo de prevención y organización del regreso a la actividad lectiva en los centros educativos de Castilla y León para el curso escolar 2020/2021

Protocolo de prevención y organización de los Servicios Complementarios y Actividades Extraescolares en los centros educativos de Castilla y León para el curso escolar 2020/2021

CASTILLA-LA MANCHA

Portal web de Educación

Resolución de 23/07/2020, de la Consejería de Educación, Cultura y Deportes, por la que se dictan instrucciones sobre medidas educativas para el curso 2020-2021 en la comunidad autónoma de Castilla-La Mancha.

INSTRUCCIÓN SOBRE LAS MEDIDAS DE PREVENCIÓN, HIGIENE Y PROMOCIÓN DE LA SALUD FRENTE AL COVID-19 PARA LOS CENTROS EDUCATIVOS DE CASTILLA LA MANCHA PARA EL PLAN DE INICIO DEL CURSO 2020-2021

Prevención de Riesgos Laborales

CATALUÑA

Portal web de la Consejería de Educación y Formación

Plan de actuación para los centros educativos para el curso 2020-2021

COMUNITAT VALENCIANA

Portal web de la Conselleria de Educación, Cultura y Deporte

Protocolo de protección y prevención frente a la transmisión y contagio del SARS-CoV-2 para centros educativos que impartan enseñanzas no universitarias en el curso 2020-2021

EXTREMADURA

Potal web de la Consejería de Educación y Empleo

Guía general para la organización y desarrollo de la actividad educativa para el curso 2020/2021 en todos los centros sostenidos con fondos públicos de la Comunidad Autonoma de Extremadura

GALICIA

Portal web de la Consellería de Educación, Universidade e Formación Profesional

Medidas educativas que se deben adoptar en el curso académico 2020/2021, en los centros docentes de la Comunidad Autónoma de Galicia en los que se imparten las enseñanzas de EI, EP, ESO y bachillerato

Protocolo de adaptación al contexto de la covid 19 en los centros de Enseñanza no Universitaria de Galicia para el curso 2020-2021

Medidas a adoptar en todos los centros de enseñanza en relación con la pandemia COVID-19

COMUNIDAD DE MADRID

Portal web de la Consejería de Educación e Investigación

Instrucciones de comienzo de curso y como consecuencia de la declaración del estado de alarma por COVID-19

REGION DE MURCIA

Portal web de la Consejería de Educación

Instrucciones de comienzo de curso 2020-2021

COMUNIDAD FORAL DE NAVARRA

Portal web del Departamento de Educación

Plan de contingencia curso 2020-2021 posibles escenarios ante la evolución de la COVID-19

PAIS VASCO

Portal web del Departamento de Educación

Organización de centros docentes no universitarios. Organización del curso en centros públicos. Protocolo General de actuación en los centros educativos frente al coronavirus

LA RIOJA

Portal web de la Consejería de Educación y Cultura

Plan de Contingencia General para el inicio del curso 2020/2021 en la Comunidad Autónoma de La Rioja

CIUDADES AUTÓNOMAS DE CEUTA Y MELILLA

GUÍA DE MEDIDAS DE PREVENCIÓN E HIGIENE FRENTE A COVID19 PARA LA REAPERTURA PARCIAL DE CENTROS EDUCATIVOS EN CEUTA Y MELILLA EL CURSO 2019-2020

Media sources

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

Así es la lucha entre el sistema inmune y el coronavirus. El País, España

Canarias identifica el mejor test para diagnosticar el Covid-19 del mercado

Canarias probará la secuenciación genética como método diagnóstico

Cientos de científicos piden a la OMS que reconozca la transmisión aérea del coronavirus

Coronavirus contact-tracing apps: can they slow the spread of COVID-19?

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

Defensas contra la COVID-19 en sangre de 2018: la potente hipótesis de la inmunidad cruzada

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

Example of a device using UV-C for decontamination

Example of a Rapid Bio Decontamination Service, from Bioquell

Everything we know about coronavirus immunity and antibodies — and plenty we still don’t

Financial Times

How did Spain get its coronavirus response so wrong?

How sewage could reveal true scale of coronavirus outbreak

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

“Lo que sabemos ahora es que quien ha dado positivo por anticuerpos está protegido”

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

Llega la herramienta de rastreo de contagios por Covid-19 de Apple y Google: tiene el respaldo de veinte países

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

New Zealand On Alert After 4 Cases Of COVID-19 Emerge From Unknown Source

Nobel laureates and science groups demand NIH review decision to kill coronavirus gran

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

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

Radiografía de tres brotes: así se contagiaron y así podemos evitarlo

Respiratory Transmission of SARS-CoV-2: What Do We Really Know?

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

SARS-CoV-2 y COVID-19: la dificultad de nombrar un nuevo virus y la enfermedad asociada

¿Se transmite por el aire el coronavirus?

Scientists are drowning in COVID-19 papers. Can new tools keep them afloat?

The Ibuprofen Debate Reveals the Danger of Covid-19 Rumors

The Risks - Know Them - Avoid Them

The Problem With Stories About Dangerous Coronavirus Mutations

The sprint to solve coronavirus protein structures — and disarm them with drugs

We've never made a successful vaccine for a coronavirus before. This is why it's so difficult

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

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

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

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

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

Broad Institute

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

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

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

Rapid Tests

Section to highlight contributions to rapid tests production and testing.

COVID-19: immunopathology and its implications for therapy

Diagnostic Testing for Severe Acute Respiratory Syndrome–Related Coronavirus-2: A Narrative Review

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

Immunological assays for SARS-CoV-2: an analysis of available commercial tests to measure antigen and antibodies

Research Coalitions and Funding Calls

Section to collect open calls in the research funding arena.

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

COG-UK COVID Genomics UK Consortium

COV-IRT – COVID-19 International Research Team

COVID-19 Clinical Research Coalition

COVID Human Genetic Effort

COVID-19 Host Genetics Initiative

COVID-19 Testing Project

COVID-Zero Coalition

Crue Universidades Españolas, CSIC y Banco Santander lanzan el FONDO SUPERA COVID-19

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

Fast Funding for COVID-19 Science

New research projects on Coronavirus

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

SPHERES. USA-CDC SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES)

The Open COVID Pledge

WHO The Global Preparedness Monitoring Board

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.

Analysis of SteraMist ionized hydrogen peroxide technology as a method for sterilizing N95 respirators and other personal protective equipment

Aerosolized Hydrogen Peroxide Decontamination of N95 Respirators, with Fit-Testing and Virologic Confirmation of Suitability for Re-Use During the COVID-19 Pandemic

Assessing the quality of nontraditional N95 filtering face-piece respirators available during the COVID-19 pandemic

Assessment of N95 respirator decontamination and re-use for SARS-CoV-2

Association of Personal Protective Equipment Use with Successful Protection Against COVID-19 Infection Among Health Care Workers

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

CDC. Cleaning and Disinfecting Your Home

CDC. Community, Work and School: Cleaning and Disinfecting

CDC. How to Protect Yourself and Others

CDC. Use of Cloth Face Coverings to Help Slow the Spread of COVID-19

Clarificación de los diferentes tipos de mascarillas, Ministerio de Sanidad

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

Effect of various decontamination procedures on disposable N95 mask integrity and SARS-CoV-2 infectivity

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

EPA. Additional Measures to Address COVID-19 in Public Indoor Spaces

EPA. Air Cleaners, HVAC Filters and Coronavirus (COVID-19)

EPA. COVID-19, Wildfires, and Indoor Air Quality

EPA. Indoor Air in Homes and Coronavirus (COVID-19)

EPA. Science and Technical Resources related to Indoor Air and Coronavirus (COVID-19)

EPA. Ventilation and Coronavirus (COVID-19)

Face Masks Against COVID-19: An Evidence Review

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

Frequently Asked Questions for Multicooker Decontamination of N95 Respirators

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

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

N95 Mask Decontamination using Standard Hospital Sterilization Technologies

N95 Respirators and Surgical Masks (Face Masks)

Publicada la Especificación UNE para facilitar la fabricación de mascarillas higiénicas reutilizables | Descarga directa de PDF

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

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

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

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

SARS-CoV-2 Transmission and the Risk of Aerosol Generating Procedures

UV-C decontamination for N95 emergency reuse: Quantitative dose validation with photochromic indicators

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.


American Society for Microbiology COVID-19 Research Registry

American Thoracic Society COVID-19 Hub

Cell Press Coronavirus Resource Hub

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

Coronavirus: Research, Commentary, and News | Science | AAAS

COVID-19 Preprints

ELSEVIER Novel Coronavirus Resource Directory | ELSEVIER Novel Coronavirus Information Center

Download full text for data-mining: server: sftp://public@coronacontent.np.elsst.com | user: public | pass: beat_corona

ERS COVID-19 resource centre

NEJM Journal Watch

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)

Springer Nature COVID-19 Hub

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

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

A new coronavirus associated with human respiratory disease in China

A Novel Coronavirus from Patients with Pneumonia in China, 2019

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

Aerosol and surface distribution of severe acute respiratory syndrome coronavirus 2 in hospital wards, Wuhan, China, 2020

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

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

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

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

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

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

CDC Coronavirus Disease 2019 (COVID-19) publications

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

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

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

Clinical Characteristics of Coronavirus Disease 2019 in China

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

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

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

Coronavirus Disease 2019: Coronaviruses and Blood Safety

Coronavirus Disease 2019 (COVID-19) in Italy

Coronavirus Disease 2019 and Influenza

Coronavirus Infections—More Than Just the Common Cold

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

COVID-19: what is next for public health?

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

Cutaneous manifestations in COVID‐19: a first perspective

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

Dermatology staff participate in fight against Covid-19 in China

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

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

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

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

Exploring possible mechanisms for COVID‐19 induced thrombocytopenia: Unanswered Questions

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

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

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

Human leukocyte antigen susceptibility map for SARS-CoV-2

Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins

Insight into 2019 novel coronavirus — An updated interim review and lessons from SARS-CoV and MERS-CoV

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

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

Managing neonates with respiratory failure due to SARS-CoV-2 Novel 2019 coronavirus genome

Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary

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

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

Novel Coronavirus Infection in Newborn Babies Under 28 Days in China

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

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

Rates of Co-infection Between SARS-CoV-2 and Other Respiratory Pathogens

Rational use of face masks in the COVID-19 pandemic

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

Respiratory virus shedding in exhaled breath and efficacy of face masks

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

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

Scientists are drowning in COVID-19 papers. Can new tools keep them afloat?

Severe Acute Respiratory Syndrome Coronavirus 2 RNA Detected in Blood Donations

Spread of SARS-CoV-2 in the Icelandic Population

Stability of the COVID-19 virus under wet, dry and acidic conditions

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

Structure of the RNA-dependent RNA polymerase from COVID-19 virus

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

Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2)

Temporal dynamics in viral shedding and transmissibility of COVID-19

The Current and Future State of Vaccines, Antivirals and Gene Therapies Against Emerging Coronaviruses

The convalescent sera option for containing COVID-19

The trinity of COVID-19: immunity, inflammation and intervention

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

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

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

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

Understanding of COVID-19 based on current evidence

Universal Screening for SARS-CoV-2 at Delivery Could Identify Many Asymptomatic Women

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 Virological assessment of hospitalized patients with COVID-2019

Maths and Epidemiological Models

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


A Path to the End of COIVD-19 - a Mathematical Model

An SEIR Model for Assessment of Current COVID-19 Pandemic Situation in the UK

Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries

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

Google Cloud AI and Harvard Global Health Institute Collaborate on new COVID-19 forecasting model

How you can help with COVID-19 modelling

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

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

Mathematical models to guide pandemic response

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

OpenABM-Covid19: Agent-based model for modelling the Covid-19

Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period

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

SIAM Mathematics of Data Science (MDS20) Distinguished Lecture Series: David L. Donoho

Swiss Medical Weekly - Potential impact of seasonal forcing on a SARS-CoV-2 pandemic

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

The Hybrid Forecasting Method SVR-ESAR for Covid-19

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

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

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

Unraveling R0: Considerations for Public Health Applications

Wrong but Useful — What Covid-19 Epidemiologic Models Can and Cannot Tell Us

PCR related articles and other detection techniques

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


A Confirmed Case of SARS-CoV-2 Pneumonia with Routine RT-PCR Negative and Virus Variation in Guangzhou, China

A handheld point-of-care system for rapid detection of SARS-CoV-2 in under 20 minutes

A protocol for massively parallel diagnosis and genome sequencing of SARS-CoV-

A rapid, low cost, and highly sensitive SARS-CoV-2 diagnostic based on whole genome sequencing

A Scalable, Easy-to-Deploy, Protocol for Cas13-Based Detection of SARS-CoV-2 Genetic Material

A simple colorimetric molecular detection of novel coronavirus (COVID-19), an essential diagnostic tool for pandemic screening

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

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

Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19

Analysis of factors associated early diagnosis in coronavirus disease 2019 (COVID-19)

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

Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis

Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid and Reliable Detection of SARS-CoV-2

BEARmix: Basic Economical Amplification Reaction one-step RT-qPCR master mix

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

Comparing library preparation methods for SARS-CoV-2 multiplex amplicon sequencing on the Illumina MiSeq platform

Comparison of Four Molecular In Vitro Diagnostic Assays for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens

Comparison of SARS-CoV2 N gene real-time RT-PCR targets and commercially available mastermixes

Comparison of SARS-CoV2 N gene real-time RT-PCR targets and commercially available mastermixes

COVID-19 Protocolo - Grupo de investigación Neuronal Ubiquitin Pathways - UPV/EHU

CRISPR–Cas12-based detection of SARS-CoV-2

Database of SARS-CoV2-relevant control materials: Specs, Vendors, and more.

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

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

Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA

Detection of Respiratory Viruses in Sputum from Adults by Use of Automated Multiplex PCR

Developing antibody tests for SARS-CoV-2

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

Efficient high throughput SARS-CoV-2 testing to detect asymptomatic carriers

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

Evaluation of Reverse Transcription-PCR Assays for Rapid Diagnosis of Severe Acute Respiratory Syndrome Associated with a Novel Coronavirus

Evaluation of WHO listed COVID-19 qPCR primers and probe in silico with 375 SERS-CoV-2 full genome sequences

Failure of the cobas® SARS-CoV-2 (Roche) E-gene assay is associated with a C-to-T transition at position 26340 of the SARS-CoV-2 genome

FALSE-NEGATIVE RESULTS OF INITIAL RT-PCR ASSAYS FOR COVID-19: A SYSTEMATIC REVIEW

False Negative Tests for SARS-CoV-2 Infection — Challenges and Implications

Fast and accurate diagnostics from highly multiplexed sequencing assays

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

Fast SARS-CoV-2 detection protocol based on RNA precipitation and RT-qPCR in nasopharyngeal swab samples

FDA Posts New Template for At-Home and Over-the-Counter Diagnostic Tests for Use in Non-Lab Settings, Such as Homes, Offices or Schools

Genotyping SARS-CoV-2 through an interactive web application

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

In silico analysis of RT-qPCR designs recommended by WHO for detection of SARS-CoV-2 and a commercial kit validated following UNE/EN ISO 17025:2005 and two reference laboratories

LamPORE, for rapid, highly scalable, low-cost COVID-19 detection

Large-scale, in-house production of viral transport media to support SARS-CoV-2 PCR testing in a multi-hospital healthcare network during the COVID-19 pandemic

Molecular Detection of SARS-CoV-2 in Formalin Fixed Paraffin Embedded Specimens

Molecular detection of SARS-CoV-2 using a reagent-free approach

Multiplex Isothermal Amplification Coupled with Nanopore Sequencing for Rapid Detection and Mutation Surveillance of SARS-CoV-2

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

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

Organisms causing secondary pneumonias in COVID-19 patients at 5 UK ICUs as detected with the FilmArray test

Overcoming the bottleneck to widespread testing: A rapid review of nucleid acid testing approaches for COVID-19 detection

Performance of the rapid Nucleic Acid Amplification by Abbott ID NOW COVID-19 in nasopharyngeal swabs transported in viral media and dry nasal swabs, in a New York City academic institution

Pooled RNA extraction and PCR assay for efficient SARS-CoV-2 detection

Pooled RNA sample reverse transcriptase real time PCR assay for SARS CoV-2 infection: a reliable, faster and economical method

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

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

Preliminary support for a 'dry swab, extraction free' protocol for SARS-CoV-2 testing via RT-qPCR

Rapid and quantitative detection of COVID-19 markers in micro-liter sized samples

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

Rapid diagnosis of SARS-CoV-2 infection by detecting IgG and IgM antibodies with an immunochromatographic device: a prospective single-center study

Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler

Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections

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

Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP)

Real-time colorimetric LAMP methodology for quantitative nucleic acids detection at the point-of-care

Reconstructed diagnostic sensitivity and specificity of the RT-PCR test for COVID-19

Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity

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

Resilient SARS-CoV-2 diagnostics workflows including viral heat inactivation

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

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

Saliva offers a sensitive, specific and non-invasive alternative to upper respiratory swabs for SARS-CoV-2 diagnosis

Saliva Sample as a Non-Invasive Specimen for the Diagnosis of Coronavirus Disease-2019 (COVID-19): a Cross-Sectional Study

Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs

SARS-CoV-2 detection with CRISPR diagnostics

SARS-CoV-2 Detection Using an Isothermal Amplification Reaction and a Rapid, Inexpensive Protocol for Sample Inactivation and PurificationSmart Pooled sample Testing for COVID-19: A Possible Solution for Sparsity of Test Kits

Screening for SARS-CoV-2 infections with colorimetric RT-LAMP and LAMP sequencing

Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection

Swabs Collected by Patients or Health Care Workers for SARS-CoV-2 Testing

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

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

Pooling and Group Testing

Subsection dedicated to pooling of samples to apply PCR (RT-qPCR) to groups of individuals.


A Note on Double Pooling Tests

Assessment of sample pooling for clinical SARS-CoV-2 testing

Evaluation of commercial qPCR kits for detection of SARS-CoV-2 in pooled samples

Evaluation of COVID-19 RT-qPCR Test in Multi sample Pools

Early detection of superspreaders by mass group pool testing can mitigate COVID-19 pandemic

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

Efficient prevalence estimation and infected sample identification with group testing for SARS-CoV-2

Efficient sample pooling strategies for COVID-19 data gathering

Evaluation of COVID-19 RT-qPCR Test in Multi sample Pools

Evaluation of Group Testing for SARS-CoV-2 RNA

Evaluation of Pool-based Testing Approaches to Enable Population-wide Screening for COVID-19

Evaluation of Sample Pooling for Screening of SARS-CoV-2

False-Negative Mitigation in Group Testing for COVID-19 Screening

Increasing testing throughput and case detection with a pooled-sample Bayesian approach in the context of COVID-19

Group testing against Covid-19

Group Testing for Estimation

Group testing for SARS-CoV-2 allows for up to 10-fold efficiency increase across realistic scenarios and testing strategies

Group testing performance evaluation for SARS-CoV-2 massive scale screening and testing

Increased PCR screening capacity using a multi-replicate pooling scheme

Increasing testing throughput and case detection with a pooled-sample Bayesian approach in the context of COVID-19

Increasing Virus Test Capacity via Recursive Pool Testing with an Application to SARS-CoV-2 Testing

LAMP-Seq: Population-Scale COVID-19 Diagnostics Using Combinatorial Barcoding

Large-scale implementation of pooled RNA-extraction and RT-PCR for SARS-CoV-2 detection

Methodology for estimating point prevalence of SARS-CoV-2 infection by pooled RT-PCR testing

Multi-Stage Group Testing Improves Efficiency of Large-Scale COVID-19 Screening

Nanotrap® particles improve detection of SARS-CoV-2 for pooled sample methods, extraction-free saliva methods, and extraction-free transport medium methods

Noisy Pooled PCR for Virus Testing

Optimal Pool Size for COVID-19 Group Testing

Optimally Pooled Viral Testing

Optimal group based testing strategy for detecting infected individuals: comparison of algorithms

Optimal sample pooling: an efficient tool against SARS-CoV-2

Optimal Size of COVID-19 Testing Pools

Optimal size of sample pooling for RNA pool testing: an avant-garde for scaling up SARS CoV 2 testing

Pooled testing with replication: a mass testing strategy for the COVID-19 pandemics

Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2

Pooling of Samples to Increase Testing Capacity for COVID-19

Rapid, Large-Scale, and Effective Detection of COVID-19 Via Non-Adaptive Testing

Recommendations for sample pooling on the Cepheid GeneXpert® system using the Cepheid Xpert® Xpress SARS-CoV-2 assay

Remarks on pooling Coronavirus tests

Sample Pooling as an efficient strategy for SARS-COV-2 RT-PCR screening: a multicenter study in Spain

Sample pooling on triplets to speed up SARS-CoV-2 diagnosis using CDC FDA EUA RT-qPCR kit

SCALE19: A scalable and cost-efficient method for testing Covid-19 based on hierarchical group testing

Sequential informed pooling approach to detect SARS-CoV2 infection

Smart Pooling: AI-powered COVID-19 testing

Statistical methods for batch screening of input populations by stage and group in COVID-19 nucleic acid testing

Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing

The brief comparison of the operational efficiency of pool-testing strategies for COVID-19 mass testing in PCR laboratories

The Mathematics of Mass Testing for COVID-19

Throat wash as a source of SARS-CoV-2 RNA to monitor community spread of COVID-19

Saliva based testing

Subsection dedicated to testing of SARS-CoV-2 based on saliva samples.


A community-deployable SARS-CoV-2 screening test using raw saliva with 45 minutes sample-to-results turnaround

Assessment of the use and quick preparation of saliva for rapid microbiological diagnosis of COVID-19

Assessment of multiplex digital droplet RT-PCR as an accurate diagnosis tool for SARS-CoV-2 detection in nasopharyngeal swabs and saliva samples

Clinical evaluation of self-collected saliva by RT-qPCR, direct RT-qPCR, RT-LAMP, and a rapid antigen test to diagnose COVID-19

Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva

COVID-19 serology at population scale: SARS-CoV-2-specific antibody responses in saliva

Detection of antibodies to the SARS-CoV-2 spike glycoprotein in both serum and saliva enhances detection of infection

Does sampling saliva increase detection of SARS-CoV-2 by RT-PCR? Comparing saliva with oro-nasopharyngeal swabs

EasyCOV: LAMP based rapid detection of SARS-CoV-2 in saliva

Evaluation of specimen types and saliva stabilization solutions for SARS-CoV-2 testing

Evaluation of symptomatic patient saliva as a sample type for the Abbott ID NOW COVID-19 assay

Field-deployable, rapid diagnostic testing of saliva samples for SARS-CoV-2

Handyfuge-LAMP: low-cost and electricity-free centrifugation for isothermal SARS-CoV-2 detection in saliva

Immunochromatographic test for the detection of SARS-CoV-2 in saliva

Preliminary optimisation of a simplified sample preparation method to permit direct detection of SARS-CoV-2 within saliva samples using reverse-transcription loop-mediated isothermal amplification (RT-LAMP)

Quantification of SARS-CoV-2 viral copy number in saliva mouthwash samples using digital droplet PCR

Rapid and extraction-free detection of SARS-CoV-2 from saliva with colorimetric LAMP

Saliva as a Candidate for COVID-19 Diagnostic Testing: A Meta-Analysis

Saliva as a non-invasive sample for the detection of SARS-CoV-2: a systematic review

Saliva is less sensitive than nasopharyngeal swabs for COVID-19 detection in the community setting

Saliva offers a sensitive, specific and non-invasive alternative to upper respiratory swabs for SARS-CoV-2 diagnosis

Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs

SalivaDirect: Simple and sensitive molecular diagnostic test for SARS-CoV-2 surveillance

Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices

Validation of a Self-administrable, Saliva-based RT-qPCR Test Detecting SARS-CoV-2

School and other human-populated spaces reopening

A Georgia sleepaway camp's coronavirus outbreak is a warning for what could happen when schools reopen, CDC says

A large COVID-19 outbreak in a high school 10 days after schools’ reopening, Israel, May 2020

A school outbreak of Norwalk-like virus: evidence for airborne transmission

A School Reopens, and the Coronavirus Creeps In

After Reopening Schools, Israel Orders Them To Shut If COVID-19 Cases Are Discovered

American Academy of Pediatrics. COVID-19 Planning Considerations: Guidance for School Re-entry

Association Between Statewide School Closure and COVID-19 Incidence and Mortality in the US

Comparison of viral levels in individuals with or without symptoms at time of COVID-19 testing among 32,480 residents and staff of nursing homes and assisted living facilities in Massachusetts

Coronavirus Disease Outbreak in Call Center, South Korea

Covid-19: German high school tests students twice a week

COVID-19 screening strategies that permit the safe re-opening of college campuses

Dozens of Australian schools shut down after coronavirus outbreaks

GOV.UK Guidance. Actions for schools during the coronavirus outbreak

Indoor transmission of SARS-CoV-2

On the effect of age on the transmission of SARS-CoV-2 in households, schools and the community

SARS-CoV-2 and the Role of Orofecal Transmission: Systematic Review

SARS-CoV-2 Transmission and Infection Among Attendees of an Overnight Camp — Georgia, June 2020

Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans

School closure and management practices during coronavirus outbreaks including COVID-19: a rapid systematic review

The risk of COVID-19 transmission in train passengers: an epidemiological and modelling study

The role of children in the spread of COVID-19: Using household data from Bnei Brak, Israel, to estimate the relative susceptibility and infectivity of children

UNESCO Education: From disruption to recovery

Was school closure effective in mitigating coronavirus disease 2019 (COVID-19)? Time series analysis using Bayesian inference

Weekly Coronavirus Disease 2019 (COVID-19) Surveillance Report Summary of COVID-19 surveillance systems Year: 2020 Week: 26

WHO Considerations for school-related public health measures in the context of COVID-19

Sciencific Data and Resources

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

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

Artic Network

Bioinformatics Unit of Instituto de Salud Carlos III (Spain)

Bioinformatics resources for SARS-CoV-2

Broad COVID-19 Testing Dashboard

CIVIO datos Pruebas PCR para detectar casos de coronavirus. Actualización diaria con el número (total y relativo) de PCR realizadas por comunidades autónomas para diagnosticar casos de covid-19

Clustering COVID-19 research papers

COG-UK The New Microreact dashboard

Coinfections in COVID-19

CORD-19. COVID-19 Open Research Dataset

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

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

COVID-19 Collaboration Platform

COVID-19 Data Hub. Funded by the Institute for Data Valorization IVADO, Canada

Coronavirus Structural Task Force

COVID-19 3D visualizer

COVID-19 Data Portal

COVID-19 Host Genetics Initiative

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

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

COVID-19 databoard ISCIII

COVID-19 GENOTYPING TOOL (Genotyping SARS-CoV-2 through an interactive web application)

COVID-19: Government Response Stringency Index

COVID-19 Law Lab collecting legal documents from the COVID-19 response

COVID-19 scenarios

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

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

DataStudio International-Domestic spreading of 2019-nCoV-V4

Databriks data collection

Datadista data on COVID-19

Dashboard del Sistema para la Vigilancia de la mortalidad diaria por todas las causas en España (Informe MoMo)

Discourse Data Against Covid19

GISAID

EMBL-EBI COVID-19 Portal

Epidemic Calculator

ESTUDIO ENE-COVID19: PRIMERA RONDA. ESTUDIO NACIONAL DE SERO-EPIDEMIOLOGÍA DE LA INFECCIÓN POR SARS-COV-2 EN ESPAÑA. INFORME PRELIMINAR 13 DE MAYO DE 2020

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

European mortality monitoring: EUROMOMO

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)

European Lung Foundation COVID-19) data center

European Virus Archive Global

Evolución del coronavirus (COVID-19) en Euskadi

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

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

IHME, Institute for Health Metrics and Evaluation, USA data

Imperial College London reports

INB/ELIXIR-ES nodes and TransBioNet members effort on COVID-19 research

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

IRRD COVID-19 em tempo real

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

MIDAS 2019 Novel Coronavirus Repository

Ministerio de Sanidad, España

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

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

NIH Coronavirus Disease 2019 Situation Summary

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

Nextstrain. Real-time tracking of pathogen evolution

NIH Open-Access Data and Computational Resources to Address COVID-19

NIKKEI ASIAN REVIEW. Coronavirus infection tracker -World Map-

OpenTargets COVID-19 repository

PolyMath COVID-19 dataset clearinghouse

Reich Lab COVID-19 Forecast Hub

Rivas Lab analysis of existing data

SAFECAST COVID-19 TESTING MAP

SARS-CoV-2 Alignment Screen

SARS-CoV-2 Galaxy Project

SARS-CoV-2 pathways

SARS-CoV-2 Sequencing Resources

SWISSMODEL homology models

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

Tout sur SARS-Cov-2 / COVID-19 à l'Institut Psteur

Virological

UCSC COVID browser

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

United Against COVID-19

Universidad de Granada - Genyo DatAC: Data Against COVID-19

Virus Pathogen Resource: VIPR SARS-CoV-2 resource (tools for sequence and structure analysis, comparative genomics and phenotype studies)

WHO updates COVID-19 dashboard with better data visualization

World-o-Meter

Zoic Labs and The Krogan Lab SARS-Cov-2 Virus-HUman Protein-Protein Interaction Map

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

Autonomous Regions and Cities in Spain:

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

Seroprevalence

New section on April 26, 2020.

A case of a readmitted patient who recovered from COVID-19 in Chengdu, China

A serological assay to detect SARS-CoV-2 seroconversion in humans

A serological assay to detect SARS-CoV-2 seroconversion in humans

A Statistical Analysis Of CoV-19 Positive Test Frequency Data Indicates A Need For Greater Attention To CoV-19 Test Quality And Pre-Wuhan Cov-19 Prevalence

Considering how biological sex impacts immune responses and COVID-19 outcomes

Coronavirus: los primeros datos de seroprevalencia estiman que un 5% de la población ha estado contagiada, con variabilidad según provincias | INFORME

COVID-19 and Postinfection Immunity. Limited Evidence, Many Remaining Questions

COVID-19 Antibody Seroprevalence in Santa Clara County, California

Daily viral kinetics and innate and adaptive immune responses assessment in COVID-19: a case series

Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals

Diagnostic accuracy of serological tests for covid-19: systematic review and meta-analysis

Disappearance of antibodies to SARS-CoV-2 in a Covid-19 patient after recovery

Different pattern of pre-existing SARS-COV-2 specific T cell immunity in SARS-recovered and uninfected individuals

Dissecting antibody-mediated protection against SARS-CoV-2

Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants

Estimating COVID-19 Antibody Seroprevalence in Santa Clara County, California. A re-analysis of Bendavid et al.

Estimation of SARS-CoV-2 infection fatality rate by real-time antibody screening of blood donors

Estimating population immunity without serological testing

Humoral immune response and prolonged PCR positivity in a cohort of 1343 SARS-CoV 2 patients in the New York City region

Humoral Response Dynamics Following Infection with SARS-CoV-2

Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection

Immune evasion via SARS-CoV-2 ORF8 protein?

Immunogenicity and Safety of a SARS-CoV-2 Inactivated Vaccine in Healthy Adults Aged 18-59 years: Report of the Randomized, Double-blind, and Placebo-controlled Phase 2 Clinical Trial

Longitudinal analyses reveal immunological misfiring in severe COVID-19

Long-Term Persistence of IgG Antibodies in SARS-CoV Infected Healthcare Workers

Performance Characteristics of the Abbott Architect SARS-CoV-2 IgG Assay and Seroprevalence Testing in Idaho

Phenotype of SARS-CoV-2-specific T-cells in COVID-19 patients with acute respiratory distress syndrome

Pre-existing immunity to SARS-CoV-2: the knowns and unknowns

Potent neutralizing antibodies against SARS-CoV-2 identified by high-throughput single-cell sequencing of convalescent patients’ B cells

Presence of SARS-CoV-2 reactive T cells in COVID-19 patients and healthy donors

Prevalence of SARS-CoV-2 in Spain (ENE-COVID): a nationwide, population-based seroepidemiological study

Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19

SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19

SARS‐CoV‐2 Seroconversion in Humans: A Detailed Protocol for a Serological Assay, Antigen Production, and Test Setup

SARS-CoV-2 seroprevalence in COVID-19 hotspots

Seroprevalence of antibodies against SARS-CoV-2 among health care workers in a large Spanish reference hospital

Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals

Test performance evaluation of SARS-CoV-2 serological assays

The potential danger of suboptimal antibody responses in COVID-19

Towards the next phase: evaluation of serological assays for diagnostics and exposure assessment

Transient IgA, steady IgG?

Viral RNA level, serum antibody responses, and transmission risk in discharged COVID-19 patients with recurrent positive SARS-CoV-2 RNA test results: a population-based observational cohort study

Sequencing, Sequences and Bioinformatics

A section of sequencing protocols, sequence sources and related bioinformatics pipelines

A High-Coverage SARS-CoV-2 Genome Sequence Acquired by Target Capture Sequencing

Alternative Illumina protocol for SARS sequencing (for Ct up to 38)

Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19

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

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

Characterization of intra-host SARS-CoV-2 variants improves phylogenomics reconstruction and may reveal functionally convergent mutations

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

CDC GitHub SARS-CoV-2 Sequencing Resources

CoV Genome Tracker: tracing genomic footprints of Covid-19 pandemic

Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event

COVID-19 ARTIC v3 Illumina library construction and sequencing protocol

COVID-19 Cell Atlas

Elevated Plasmin(ogen) as a Common Risk Factor for COVID-19 Susceptibility

Emergence of multiple variants of SARS-CoV-2 with signature structural changes

Enrichment workflow for detecting coronavirus using Illumina NGS systems

High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs

How fast does the SARS-Cov-2 virus really mutate in heterogeneous populations?

iVar for for viral amplicon-based sequencing

Katarina Braun GitHub ARS-CoV-2_sequencing repository

Nanopore sequencing enables comprehensive transposable element epigenomic profiling

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

Partner independent fusion gene detection by multiplexed CRISPR-Cas9 enrichment and long read nanopore sequencing

Rapid and Inexpensive Whole-Genome Sequencing of SARS-CoV-2 using 1200 bp Tiled Amplicons and Oxford Nanopore Rapid Barcoding

Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands

Quality control of low-frequency variants in SARS-CoV-2 genomes

SARS coronavirus 2 in Viral Zone / Covid-19 genome expression

Sequence characterization and molecular modeling of clinically relevant variants of the SARS-CoV-2 main protease

Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing

The global population of SARS-CoV-2 is composed of six major subtypes

Specific mutations in SARS-CoV2 RNA dependent RNA polymerase and helicase alter protein structure, dynamics and thus function: Effect on viral RNA replication

Shiny and R related dashboards and packages

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

R Interface to COVID-19 Data Hub

Vaccines

Section under construction...

Draft landscape of COVID-19 candidate vaccines

Virology

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

A gene locus that controls expression of ACE2 in virus infection

A novel bat coronavirus closely related to SARS-CoV-2 contains natural insertions at the S1/S2 cleavage site of the spike protein

A previously uncharacterized gene in SARS-CoV-2 and the origins of the COVID-19 pandemic

Another Decade, Another Coronavirus

A single-cell atlas of the peripheral immune response to severe COVID-19

ACE2 and TMPRSS2 variants and expression as candidates to sex and country differences in COVID-19 severity in Italy

ACE2: from vasopeptidase to SARS virus receptor

ACE2 Receptor Expression and Severe Acute Respiratory Syndrome Coronavirus Infection Depend on Differentiation of Human Airway Epithelia

ACE2 shedding and furin abundance in target organs may influence the efficiency of SARS-CoV-2 entry

ACE2: The Only Thing That Matters?

A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV

Airway expression of SARS-CoV-2 receptor, ACE2, and proteases, TMPRSS2 and furin, in severe asthma

Analysis the susceptibility of lung cancer patients to SARS-CoV-2 infection

Angiotensin‐converting enzyme 2 (ACE2) as a SARS‐CoV‐2 receptor: molecular mechanisms and potential therapeutic target

Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus

Angiotensin Converting Enzyme 2: SARS-CoV-2 Receptor and Regulator of the Renin-Angiotensin System

Angiotensin receptor blockers as tentative SARS-CoV-2 therapeutics

A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin

A Unique Protease Cleavage Site Predicted in the Spike Protein of the Novel Pneumonia Coronavirus (2019-nCoV) Potentially Related to Viral Transmissibility

Bioinformatics Study on Structural Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2) For Better Understanding the Vaccine Development

CD147/EMMPRIN Acts as a Functional Entry Receptor for Measles Virus on Epithelial Cells

Characterization of intra-host SARS-CoV-2 variants improves phylogenomic reconstruction and may reveal functionally convergent mutations

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

Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV

Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine

Comparative computational analysis of SARS-CoV-2 nucleocapsid protein epitopes in taxonomically related coronaviruses

Comparison of Commercially Available and Laboratory Developed Assays for in vitro Detection of SARS-CoV-2 in Clinical Laboratories

Complement as a target in COVID-19?

Comprehensive characterization of N- and O- glycosylation of SARS-CoV-2 human receptor angiotensin converting enzyme 2

Coronavirus envelope protein: current knowledge

Coronavirus infections and immune responses

COVID‐19 in the heart and the lungs: could we “Notch” the inflammatory storm?

COVID-19. Transport of respiratory droplets in a microclimatologic urban scenario

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

Cyclophilin–CD147 interactions: a new target for anti-inflammatory therapeutics

Elevated Plasmin(ogen) as a Common Risk Factor for COVID-19 Susceptibility

Elucidating the differences in the molecular mechanism of receptor binding between 2019-nCoV and the SARS-CoV viruses using computational tools

Emerging WuHan (COVID-19) coronavirus: glycan shield and structure prediction of spike glycoprotein and its interaction with human CD26

Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells

Evidence of the COVID-19 Virus Targeting the CNS: Tissue Distribution, Host–Virus Interaction, and Proposed Neurotropic Mechanisms

Evolutionary stasis of viruses? | Reply to ‘Evolutionary stasis of viruses?’

Estimating SARS-CoV-2 seroprevalence and epidemiological parameters with uncertainty from serological surveys

Evaluation of antibody testing for SARS-Cov-2 using ELISA and lateral flow immunoassays

Expression of SARS-CoV-2 receptor ACE2 and the spike protein processing enzymes in developing human embryos

Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event

Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses

Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Human ACE2 receptor polymorphisms predict SARS-CoV-2 susceptibility

Infection of dogs with SARS-CoV-2

Individual variation of the SARS-CoV2 receptor ACE2 gene expression and regulation

Immune mechanisms of pulmonary intravascular coagulopathy in COVID-19 pneumonia

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

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Interaction of drugs candidates with various SARS-CoV-2 receptors: an in silico study to combat COVID-19

Is COVID-19 receiving ADE from other coronaviruses?

Isolation and characterization of SARS-CoV-2 from the first US COVID-19 patient

Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins

Mechanistic modeling of the SARS-CoV-2 disease map

Meplazumab treats COVID-19 pneumonia: an open-labelled, concurrent controlled add-on clinical trial

Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino-acid deletion in nsp2 (Asp268Del)

Novel ACE2-Independent Carbohydrate-Binding of SARS-CoV-2 Spike Protein to Host Lectins and Lung Microbiota

Origin and evolution of pathogenic coronaviruses

Pandemics: spend on surveillance, not prediction

Persistent viral shedding of SARS-CoV-2 in faeces - a rapid review

Predicting the angiotensin converting enzyme 2 (ACE2) utilizing capability as the receptor of SARS-CoV-2

Prisoners of war — host adaptation and its constraints on virus evolution

Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak

Profile of a killer: the complex biology powering the coronavirus pandemic

Ready, Set, Fuse! The Coronavirus Spike Protein and Acquisition of Fusion Competence

Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus

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

SARS Coronavirus Redux

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

SARS-CoV-2 infects T lymphocytes through its spike protein-mediated membrane fusion

SARS-CoV-2 invades host cells via a novel route: CD147-spike protein

SARS-CoV-2 Life Cycle: Stages and Inhibition Targets

SARS-CoV-2 productively infects human gut enterocytes

SARS-CoV-2 receptor ACE2 and TMPRSS2 are predominantly expressed in a transient secretory cell type in subsegmental bronchial branches

SARS-CoV-2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells

Should COVID-19 Concern Nephrologists? Why and to What Extent? The Emerging Impasse of Angiotensin Blockade

Single-cell analysis of human lung epithelia reveals concomitant expression of the SARS-CoV-2 receptor ACE2 with multiple virus receptors and scavengers in alveolar type II cells

Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir

Structural basis of receptor cognition by SARS-CoV-2

Structural Basis of SARS-CoV-2 Spike Protein Priming by TMPRSS2

Structural analysis of SARS-CoV-2 and predictions of the human interactome

Structural interactions between pandemic SARS-CoV-2 spike glycoprotein and human Furin protease

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

Structure of replicating SARS-CoV-2 polymerase

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

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

Targeting the Endocytic Pathway and Autophagy Process as a Novel Therapeutic Strategy in COVID-19

Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study

The biology of influenza viruses

The insert sequence in SARS-CoV-2 enhances spike protein cleavage by TMPRSS

The proximal origin of SARS-CoV-2

The SARS-CoV-2 receptor-binding domain elicits a potent neutralizing response without antibody-dependent enhancement

TMPRSS2 and ADAM17 Cleave ACE2 Differentially and Only Proteolysis by TMPRSS2 Augments Entry Driven by the Severe Acute Respiratory Syndrome Coronavirus Spike Protein

TMPRSS2 and TMPRSS4 mediate SARS-CoV-2 infection of human small intestinal enterocytes

Tracking changes in SARS-CoV-2 Spike: evidence that D614G increases infectivity of the COVID-19 virus

Tracking virus outbreaks in the twenty-first century

Tropism, replication competence, and innate immune responses of the coronavirus SARS-CoV-2 in human respiratory tract and conjunctiva: an analysis in ex-vivo and in-vitro cultures

Understanding SARS-CoV-2-Mediated Inflammatory Responses: From Mechanisms to Potential Therapeutic Tools

Unveiling diffusion pattern and structural impact of the most invasive SARS-CoV-2 spike mutation

Viral and host factors related to the clinical outcome of COVID-19

Viral dynamics in mild and severe cases of COVID-19

Viral load of SARS-CoV-2 in clinical samples

We shouldn’t worry when a virus mutates during disease outbreaks

Why do RNA viruses recombine?

Widely available lysosome targeting agents should be considered as a potential therapy for COVID-19

Animal Models & Epizootic Infections

A Comprehensive Review of Animal Models for Coronaviruses: SARS-CoV-2, SARS-CoV, and MERS-CoV

A Mouse Model of SARS-CoV-2 Infection and Pathogenesis

A SARS-CoV-2 Infection Model in Mice Demonstrates Protection by Neutralizing Antibodies

A versatile mouse model of COVID-19

Antiviral Efficacies of FDA-Approved Drugs against SARS-CoV-2 Infection in Ferrets

ARDS and Cytokine Storm in SARS-CoV-2 Infected Caribbean Vervets

Comparison of Transgenic and Adenovirus hACE2 Mouse Models for SARS-CoV-2 Infection

Comparative pathogenesis of COVID-19, MERS, and SARS in a nonhuman primate model

Comparison of SARS-CoV-2 spike protein binding to ACE2 receptors from human, pets, farm animals, and putative intermediate hosts

Establishment of an African green monkey model for COVID-19

Infection and Rapid Transmission of SARS-CoV-2 in Ferret

Infection of bat and human intestinal organoids by SARS-CoV-2

Infection of dogs with SARS-CoV-2

Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters

Pathogenesis and transmission of SARS-CoV-2 in golden hamsters

Primary exposure to SARS-CoV-2 protects against reinfection in rhesus macaques

Proteomics of SARS-CoV-2-infected host cells reveals therapy targets

SARS-CoV-2 infection induces germinal center responses with robust stimulation of CD4 T follicular helper cells in rhesus macaques

SARS-CoV-2 infects and damages the mature and immature olfactory sensory neurons of hamsters

Simulation of the clinical and pathological manifestations of Coronavirus Disease 2019 (COVID-19) in golden Syrian hamster model: implications for disease pathogenesis and transmissibility

Susceptibility of ferrets, cats, dogs, and other domesticated animals to SARS–coronavirus 2

The Role of Host Genetic Factors in Coronavirus Susceptibility: Review of Animal and Systematic Review of Human Literature

Evolution & Phylogenetics

A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology

A new coronavirus associated with human respiratory disease in China

A planarian nidovirus expands the limits of RNA genome size

A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence

ACE2 diversity in placental mammals reveals the evolutionary strategy of SARS-CoV-2

Analysis of Rapidly Emerging Variants in Structured Regions of the SARS-CoV-2 Genome

Assembly of an integrated human lung cell atlas reveals that SARS-CoV-2 receptor is co-expressed with key elements of the kinin-kallikrein, renin-angiotensin and coagulation systems in alveolar cells

Complex Immune Dysregulation in COVID-19 Patients with Severe Respiratory Failure

Conserved Genomic Terminals of SARS-CoV-2 as Co-evolving Functional Elements and Potential Therapeutic Targets

Equine arteritis virus is not a togavirus but belongs to the coronaviruslike superfamily

Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation

Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans

Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico

High‐Coverage SARS‐CoV‐2 Genome Sequences Acquired by Target Capture Sequencing

Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates

Identification of super-transmitters of SARS-CoV-2

Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins

Infection and Rapid Transmission of SARS-CoV-2 in Ferrets

Genotyping coronavirus SARS-CoV-2: Methods and implications

Pathological findings of COVID-19 associated with acute respiratory distress syndrome

Possible Bat Origin of Severe Acute Respiratory Syndrome Coronavirus 2

Rampant C→U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories

Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands

RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look

Sarbecovirus comparative genomics elucidates gene content of SARS-CoV-2 and functional impact of COVID-19 pandemic mutations

SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects

SARS-CoV-2 (COVID-19) structural and evolutionary dynamicome: Insights into functional evolution and human genomics

Six reference-quality genomes reveal evolution of bat adaptations

Snapshot of the evolution and mutation patterns of SARS-CoV-2

Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2

The D614G mutation of SARS-CoV-2 spike protein enhances viral infectivity and decreases neutralization sensitivity to individual convalescent sera

The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses

Virus Isolation from the First Patient with SARS-CoV-2 in Korea

Host Immune Response

A possible role of immunopathogenesis in COVID-19 progression

A SARS-CoV-2 serological assay to determine the presence of blocking antibodies that compete for human ACE2 binding

An inflammatory cytokine signature helps predict COVID-19 severity and death

Analysis of a SARS-CoV-2-Infected Individual Reveals Development of Potent Neutralizing Antibodies with Limited Somatic Mutation

Anti-Spike, anti-Nucleocapsid and neutralizing antibodies in SARS-CoV-2 hospitalized patients and asymptomatic carriers

Autoinflammatory and autoimmune conditions at the crossroad of COVID-19

Beyond the Spike: identification of viral targets of the antibody response to SARS-CoV-2 in COVID-19 patients

Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent COVID-19 patients

CD8+ T cell cross-reactivity against SARS-CoV-2 conferred by other coronavirus strains and influenza virus

Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections

Comprehensive mapping of immune perturbations associated with severe COVID-19

Convergent antibody responses to SARS-CoV-2 in convalescent individuals

COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis

Critical Role of Type III Interferon in Controlling SARS-CoV-2 Infection in Human Intestinal Epithelial Cells

Cross-reactive antibody response between SARS-CoV-2 and SARS-CoV infections

Cross-sectional evaluation of humoral responses against SARS-CoV-2 Spike

Cross-talk between the airway epithelium and activated immune cells defines severity in COVID-19

Cytokine biomarkers of COVID-19

Deep immune profiling of COVID-19 patients reveals distinct immunotypes with therapeutic implications

Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures

Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals

Down-regulated gene expression spectrum and immune responses changed during the disease progression in COVID-19 patients

Dynamic changes of D-dimer and neutrophil-lymphocyte count ratio as prognostic biomarkers in COVID-19

Elevated Glucose Levels Favor SARS-CoV-2 Infection and Monocyte Response through a HIF-1α/Glycolysis-Dependent Axis

Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions

Evidence for structural protein damage and membrane lipid remodeling in red blood cells from COVID-19 patients

Gut microbiota may underlie the predisposition of healthy individuals to COVID-19

High levels of SARS-CoV-2 specific T-cells with restricted functionality in patients with severe course of COVID-19

High seroprevalence for SARS-CoV-2 among household members of essential workers detected using a dried blood spot assay

Homologous 2′,5′-phosphodiesterases from disparate RNA viruses antagonize antiviral innate immunity

Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2

Humoral immune response and prolonged PCR positivity in a cohort of 1343 SARS-CoV 2 patients in the New York City region

IgA dominates the early neutralizing antibody response to SARS-CoV-2

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

Impaired immune cell cytotoxicity in severe COVID-19 is IL-6 dependent

Immunogenic profile of SARS-CoV-2 spike in individuals recovered from COVID-19

Immune Response to SARS-CoV-2 and Mechanisms of Immunopathological Changes in COVID-19

Longitudinal immune profiling reveals distinct features of COVID-19 pathogenesis

Longitudinal COVID-19 profiling associates IL-1Ra and IL-10 with disease severity and RANTES with mild disease

Modulation of Extracellular ISG15 Signaling by Pathogens and Viral Effector Proteins

Mouse model of SARS-CoV-2 reveals inflammatory role of type I interferon signaling

Mutations from bat ACE2 orthologs markedly enhance ACE2-Fc neutralization of SARS-CoV-2

Phenotype and kinetics of SARS-CoV-2-specific T cells in COVID-19 patients with acute respiratory distress syndrome

Platelet activation and platelet-monocyte aggregates formation trigger tissue factor expression in severe COVID-19 patients

Potently neutralizing and protective human antibodies against SARS-CoV-2

Profiling serum cytokines in COVID-19 patients reveals IL-6 and IL-10 are disease severity predictors

Proteomics Uncovers Immunosuppression in COVID-19 Patients with Long Disease Course

SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors

SARS-CoV-2 Infection of Pluripotent Stem Cell-derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response

SARS-CoV-2 proteome microarray for global profiling of COVID-19 specific IgG and IgM responses

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

SARS-CoV-2-specific T cells exhibit unique features characterized by robust helper function, lack of terminal differentiation, and high proliferative potential

SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls

SARS-CoV-2 viral loads and serum IgA/IgG immune responses in critically ill COVID-19 patients

Serum protein profiling reveals a landscape of inflammation and immune signaling in early-stage COVID-19 infection

Severe SARS-CoV-2 infection in humans is defined by a shift in the serum lipidome resulting in dysregulation of eicosanoid immune mediators

Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19

Single-Cell Omics Reveals Dyssynchrony of the Innate and Adaptive Immune System in Progressive COVID-19

Single-cell transcriptomic analysis of SARS-CoV-2 reactive CD4 + T cells

Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection

Study on the expression levels of antibodies against SARS-CoV-2 at different period of disease and its related factors in 192 cases of COVID-19 patients

Symptomatic SARS-CoV-2 infections display specific IgG Fc structures

Targeted Immunosuppression Distinguishes COVID-19 from Influenza in Moderate and Severe Disease

Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals

The Dynamic Changes of Antibodies against SARS-CoV-2 during the Infection and Recovery of COVID-19

The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients

The SARS-CoV-2 T-cell immunity is directed against the spike, membrane, and nucleocapsid protein and associated with COVID 19 severity

Type I and III interferons disrupt lung epithelial repair during recovery from viral infection

Type III interferons disrupt the lung epithelial barrier upon viral recognition

Viral and host factors related to the clinical outcome of COVID-19

Will we see protection or reinfection in COVID-19?

Proteins & Translation

A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

Characterization of an efficient coronavirus ribosomal frameshifting signal: requirement for an RNA pseudoknot

Codon Usage and Phenotypic Divergences of SARS-CoV-2 Genes

Critical Differences Between the Binding Features of the Spike Proteins of SARS-CoV-2 and SARS-CoV

Cytologic and molecular correlates of SARS-CoV-2 infection of the nasopharynx

Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing

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

High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling

Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2

Integrative Vectors for Regulated Expression of SARS-CoV-2 Proteins Implicated in RNA Metabolism

Proteomic and Metabolomic Characterization of COVID-19 Patient Sera

RNA 3'-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10/nsp14 exoribonuclease complex

The SARS-CoV-2 spike protein alters barrier function in 2D static and 3D microfluidic in vitro models of the human blood-brain barrier

RNA Replication

A unifying structural and functional model of the coronavirus replication organelle: Tracking down RNA synthesis

Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus acquired during the early stages of human-to-human transmission

Comprehensive in-vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms

Coronaviruses: an RNA proofreading machine regulates replication fidelity and diversity

Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling

Infidelity of SARS-CoV Nsp14-Exonuclease Mutant Virus Replication Is Revealed by Complete Genome Sequencing

Nidovirales: evolving the largest RNA virus genome

One severe acute respiratory syndrome coronavirus protein complex integrates processive RNA polymerase and exonuclease activities

Ribose 2'-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5

RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus

SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum

Severe Acute Respiratory Syndrome Coronavirus 2 from Patient with 2019 Novel Coronavirus Disease, United States

Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex

Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase

Structure of replicating SARS-CoV-2 polymerase

Structure of the SARS-CoV nsp12 polymerase bound to nsp7 and nsp8 co-factors

Virus Assembly, Protein Processing and Structure

A direct RNA-protein interaction atlas of the SARS-CoV-2 RNA in infected human cells

A proposed role for the SARS-CoV-2 nucleocapsid protein in the formation and regulation of biomolecular condensates

An Infectious cDNA Clone of SARS-CoV-2

Afucosylated immunoglobulin G responses are a hallmark of enveloped virus infections and show an exacerbated phenotype in COVID-19

Architecture and self-assembly of the SARS-CoV-2 nucleocapsid protein

Companion vaccine Bioinformatic design tool reveals limited functional genomic variability of SARS-Cov-2 Spike Receptor Binding Domain

Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites

Deducing the N- and O- glycosylation profile of the spike protein of novel coronavirus SARS-CoV-2

Discovery of G-quadruplex-forming sequences in SARS-CoV-2

High-surety isothermal amplification and detection of SARS-CoV-2, including with crude enzymes Identification of common deletions in the spike protein of SARS-CoV-2

Ligand-centered assessment of SARS-CoV-2 drug target models in the Protein Data Bank

Modeling and Simulation of a Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane

Persistence of Severe Acute Respiratory Syndrome Coronavirus 2 in Aerosol Suspensions

Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically-Sensitive Activation Loop

Self-Collected Oral Fluid and Nasal Swabs Demonstrate Comparable Sensitivity to Clinician Collected Nasopharyngeal Swabs for Covid-19 Detection

Severe Acute Respiratory Syndrome Coronavirus ORF6 Antagonizes STAT1 Function by Sequestering Nuclear Import Factors on the Rough Endoplasmic Reticulum/Golgi Membrane

Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate

Structural analysis of the putative SARS-CoV-2 primase complex

Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS-CoV-2

Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine

The D614G mutation in SARS-CoV-2 Spike increases transduction of multiple human cell types

The SARS-CoV-2 conserved macrodomain is a highly efficient ADP-ribosylhydrolase enzyme

The sprint to solve coronavirus protein structures — and disarm them with drugs

Unique and Conserved Features of Genome and Proteome of SARS-coronavirus, an Early Split-off From the Coronavirus Group 2 Lineage

Viral Entry & Receptors

A glycan cluster on the SARS-CoV-2 spike ectodomain is recognized by Fab-dimerized glycan-reactive antibodies

A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells

A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2

A pH-dependent switch mediates conformational masking of SARS-CoV-2 spike

ACE2 Expression is Increased in the Lungs of Patients with Comorbidities Associated with Severe COVID-19

Controlling the SARS-CoV-2 spike glycoprotein conformation

COVID-19 Coronavirus spike protein analysis for synthetic vaccines, a peptidomimetic antagonist, and therapeutic drugs, and analysis of a proposed achilles' heel conserved region to minimize probability of escape mutations and drug resistance

Cryo-EM analysis of the post-fusion structure of the SARS-CoV spike glycoprotein

Does the human placenta express the canonical cell entry mediators for SARS-CoV-2?

Distinct conformational states of SARS-CoV-2 spike protein

Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses

Glycans on the SARS-CoV-2 Spike Control the Receptor Binding Domain Conformation

High affinity binding of SARS-CoV-2 spike protein enhances ACE2 carboxypeptidase activity

Interferons and viruses induce a novel primate-specific isoform dACE2 and not the SARS-CoV-2 receptor ACE2

Is the Rigidity of SARS-CoV-2 Spike Receptor-Binding Motif the Hallmark for Its Enhanced Infectivity? Insights from All-Atoms Simulations

Key residues of the receptor binding motif in the spike protein of SARS-CoV-2 that interact with ACE2 and neutralizing antibodies

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

LY6E impairs coronavirus fusion and confers immune control of viral disease

LY6E Restricts Entry of Human Coronaviruses, Including Currently Pandemic SARS-CoV-2

Neuropilin-1 facilitates SARS-CoV-2 cell entry and provides a possible pathway into the central nervous system

Neuropilin-1 is a host factor for SARS-CoV-2 infection

Neutralization of SARS-CoV-2 spike pseudotyped virus by recombinant ACE2-Ig

Robust ACE2 protein expression localizes to the motile cilia of the respiratory tract epithelia and is not increased by ACE inhibitors or angiotensin receptor blockers

SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract

SARS-CoV-2, SARS-CoV-1 and MERS-CoV viral load dynamics, duration of viral shedding and infectiousness: a living systematic review and meta-analysis

SARS-CoV-2 Spike protein hijacks VEGF-A/Neuropilin-1 receptor signaling to induce analgesia

SARS-CoV-2 Spike protein variant D614G increases infectivity and retains sensitivity to antibodies that target the receptor binding domain

SARS-CoV-2 viral load in the upper respiratory tract of children and adults with early acute COVID-19

Single-cell longitudinal analysis of SARS-CoV-2 infection in human bronchial epithelial cells

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

SARS-CoV-2 infection induces EMT-like molecular changes, including ZEB1-mediated repression of the viral receptor ACE2, in lung cancer models

SARS-CoV-2 productively infects human gut enterocytes

SARS‐CoV‐2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells

Shielding and Beyond: The Roles of Glycans in SARS-CoV-2 Spike Protein

Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors and suggest subtype specificity

Site-specific glycan analysis of the SARS-CoV-2 spike

Structural and functional basis of SARS-CoV-2 entry by using human ACE2

Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

Structure-based design of prefusion-stabilized SARS-CoV-2 spikes

The Global Phosphorylation Landscape of SARS-CoV-2 Infection

The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State

TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion

Viral Replicate/Non-Structural Proteins/Enzymes

An in silico map of the SARS-CoV-2 RNA Structurome

A molecular pore spans the double membrane of the coronavirus replication organelle

Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs

Crystal structures of SARS-CoV-2 ADP-ribose phosphatase (ADRP): from the apo form to ligand complexes

Crystal Structure of the SARS-CoV-2 Non-structural Protein 9, Nsp9

Genetic architecture of host proteins interacting with SARS-CoV-2

Intracellular autoactivation of TMPRSS11A, an airway epithelial transmembrane serine protease

Molecular Basis for ADP-ribose Binding to the Mac1 Domain of SARS-CoV-2 Nsp3

Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform

Replication of Severe Acute Respiratory Syndrome Coronavirus 2 in Human Respiratory Epithelium

SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology

SARS-CoV-2 nsp13, nsp14, nsp15 and orf6 function as potent interferon antagonists

Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2

Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2

Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography

The ORF3a protein of SARS-CoV-2 induces apoptosis in cells

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.

Contact us

Want to contact us? We highly encourage people to contribute to this COVID-19 repository (and acknowledged in the section above). Please, send me a Direct Message on Twitter (see below).

Last update: 15:20 GMT - August 12, 2020 | By JMLS @resocios

Update logs

August 12, 2020 updates. Two new sections on Government COVID 19 Contingency Plans for Schools Reopening and Emerging Disease Challenges, together with a bunch of additional resources: airborne transmission (3); saliva based testing (1); schools (and other human-populated spaces) reopenings (5); epidemiology (4); media sources (3); pooling and group testing (1); PCR related methods (3); research coalitions and funding calls (1); seroprevalence (1); sequencing (4)... Enjoy the reading! ;=)

August 4, 2020 updates: a new massive update since the creation of this repository: (>200 new records!): new section on airborne transmission (27); new section on saliva based testing (24); new section on schools (and other human-populated spaces) reopenings (18); clinics (5); data boards (10); educational resources (1); epidemiology (10); guidelines and reports (4); mathematical models (2); media sources (4); pooling and group testing (3); PCR related methods (9); research coalitions and funding calls (1); respirators, masks, and other Personal Protective Equipments (PPE) section (11); seroprevalence (14); sequencing (1); virology (83)... Enjoy the reading! ;=)

July 4, 2020 updates: the largest update since the creation of this repository:ç (>300 new records!): scientific literature hubs (3), data hubs (2), sequencing (5), genomics (2), new section of pooling (2), reports (2), media sources (8), mathematical models (2), PCR stuff (3), new section of apps for COVID-19 tracking (10), new section on vaccines (1), restructured section on Virology (>250), seroprevalence (5)... Enjoy the reading! ;=)

May 16, 2020 updates: a new major update with 64 new entries as follows: a new section, Clinical stuff, including the first COVID-19 autopsies (10), Data sources (10), Diagnostics (6), Epidemiology (5), Genomics (9), Maths (1), Respirators and other PPE (1), Media (2), PCR and related stuff (4), Preprints and Published literature (2), Seroprevalence (7), and Viral mechanisms (7). Enjoy the reading! ;=)

May 2, 2020 updates: a new major update with 86 new entries and a new section on Book chapters, as follows: Book chapters (5), Clinical (1), Data sources (1), Diagnostics (16), Epidemiology (12), Genomics (9), Journal COVID-19 hubs (5), Maths (1), Respirators and other PPE (1), Projects and Calls (2), Media (1), PCR and related stuff (11), Preprints and Published literature (1), Seroprevalence (9), Viral mechanisms (10), and Education (2). Enjoy the reading! ;=)

April 26, 2020 updates: new Epidemiology, Diagnostics, and Seroprevalence sections; 2 entries in Media section; 10 new entries in Virology section; 7 entries in the renamed 'Genomics and Phylodynamics' section; many (13) new entries in the PCR and related stuff (attention to new protocols and experiments for detecting the virus in sputum, use of 'dry-swabs', and saliva samples); more on funding opportunities; and some new data sources (3). Most of the entries now alphabetically sorted.

April 21, 2020 updates: CRISPR–Cas12-based detection of SARS-CoV-2.

April 20, 2020 updates: an alternative Illumina protocol for SARS sequencing (for Ct up to 38) in the Sequences & Sequencing section; new PCR fast detection method using a portable PCR thermocycler and comparative of PCR methods.

April 19, 2020 updates: 67 new selected preprints and published papers in the Viral mechanisms section courtesy of Prof. A. Valenzuela (ULL).

April 17-18, 2020 updates: new wiki structure in progress.

April 16, 2020 updates: several entries in the Scientific Literature (Preprints & Published); and two new items in data sources.

April 15, 2020 updates: added Databricks data collection; new CoV Genome Tracker; COVID-19 in Icelandic population; new records in the Education section; new articles about use and disinfection or respirators; more on virus mechanisms; new papers on COVID-19 detection techniques.

April 14, 2020 updates: more on False Negatives in qPCR, the impact of face mask against COVID-19, JAMA review of pharmacological treatments for COVID-19 in the Preprints section; added some Journals Watch pages; dashboard of the Spanish MoMo report about mortality, new dashboard for WHO, and new dashboard with graphical information for COVID-19 data in the Canary Islands by Grafcan-GOBCAN, in the Data Sources section; modeling of the SARS-CoV-2 disease map in the Viral mechanisms section; many new inputs in different sections (>20); new pages "Code of Conduct" and "Contributing to this repository" created.

April 13, 2020 updates: few new articles in Scientific Literature (Pre-prints & Peer-Reviewed Papers) section and MIDAS COVID-19 repository in the Data Sources section. As the repository increases its size, we are moving into a Wiki format (soon here!). Pull request by Miguel Correa added to the main branch of this repository.

April 12, 2020 updates: new articles regarding COVID-19 detection, a comprehensive draft list of clinical trials by country from WHO (updated 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 of non-specific PCR primers and False Negatives; more on the disinfection of respirators.

April 10, 2020 updates: new logos; new papers in Scientific 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); a 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.