Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

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Investigation of a severe SARS-CoV-2 outbreak in a long-term care home early in the pandemic

(2021) Michelle Murti et al.   CANADIAN MEDICAL ASSOCIATION JOURNAL

Outbreak investigation of symptomatic SARS-COV-2 VOC 202012/01-lineage B.1.1.7 infection in healthcare workers, Italy

(2021) Daniela Loconsole et al.   CLINICAL MICROBIOLOGY AND INFECTION

Genomic characteristics and clinical effect of the emergent SARS-CoV-2 B.1.1.7 lineage in London, UK: a whole-genome sequencing and hospital-based cohort study

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Key epidemiological drivers and impact of interventions in the 2020 SARS-CoV-2 epidemic in England

(2021) Edward S. Knock et al.   Science Translational Medicine

Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

(2021) George Githinji et al.   Nature Communications

Genomics-informed responses in the elimination of COVID-19 in Victoria, Australia: an observational, genomic epidemiological study

(2021) Courtney R Lane et al.   Lancet Public Health

Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens

(2021) Kevin S. Kuchinski et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities

(2021) Dinesh Aggarwal et al.   Lancet Microbe

An interactive web-based dashboard to track COVID-19 in real time

(2020) Ensheng Dong et al.   LANCET INFECTIOUS DISEASES

Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States

(2020) Joseph R. Fauver et al.   CELL

COVID-19 in long-term care facilities: An upcoming threat that cannot be ignored

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The proximal origin of SARS-CoV-2

(2020) Kristian G. Andersen et al.   NATURE MEDICINE

COVID-19 Among Workers in Meat and Poultry Processing Facilities ― 19 States, April 2020

(2020) Jonathan W. Dyal et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Integrating Biodiversity Infrastructure into Pathogen Discovery and Mitigation of Emerging Infectious Diseases

(2020) Joseph A Cook et al.   BIOSCIENCE

Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study

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

(2020) Bas B. Oude Munnink et al.   NATURE MEDICINE

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

(2020) Darlan S. Candido et al.   SCIENCE

COVID-19 pandemic reveals the peril of ignoring metadata standards

(2020) Lynn M. Schriml et al.   Scientific Data

SARS‐CoV‐2 outbreak investigation in a German meat processing plant

(2020) Thomas Günther et al.   EMBO Molecular Medicine

Genomic evidence for reinfection with SARS-CoV-2: a case study

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Rapid isothermal amplification and portable detection system for SARS-CoV-2

(2020) Anurup Ganguli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tracking the COVID-19 pandemic in Australia using genomics

(2020) Torsten Seemann et al.   Nature Communications

Serial Testing for SARS-CoV-2 and Virus Whole Genome Sequencing Inform Infection Risk at Two Skilled Nursing Facilities with COVID-19 Outbreaks — Minnesota, April–June 2020

(2020) Joanne Taylor et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Analysis of Genomic Characteristics and Transmission Routes of Patients With Confirmed SARS-CoV-2 in Southern California During the Early Stage of the US COVID-19 Pandemic

(2020) Wenjuan Zhang et al.   JAMA Network Open

Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

(2020) Jemma L. Geoghegan et al.   Nature Communications

Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland

(2020) Ana da Silva Filipe et al.   Nature Microbiology

PulseNet and the Changing Paradigm of Laboratory-Based Surveillance for Foodborne Diseases

(2019) Kristy A. Kubota et al.   PUBLIC HEALTH REPORTS

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

OUP accepted manuscript

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Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database

(2016) Marc W. Allard et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Standardized Metadata for Human Pathogen/Vector Genomic Sequences

(2014) Vivien G. Dugan et al.   PLoS One

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata

(2011) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

The minimum information about a genome sequence (MIGS) specification

(2008) Dawn Field et al.   NATURE BIOTECHNOLOGY