Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management

CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes

(2021) Dave J. Baker et al.   Genome Medicine

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

(2020) Roujian Lu et al.   LANCET

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

(2020) Chaolin Huang et al.   LANCET

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

(2020) Ensheng Dong et al.   LANCET INFECTIOUS DISEASES

SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients

(2020) Lirong Zou et al.   NEW ENGLAND JOURNAL OF MEDICINE

Evaluation of Transport Media and Specimen Transport Conditions for the Detection of SARS-CoV-2 Using Real Time Reverse Transcription PCR

(2020) Amy A. Rogers et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Gender Differences in Patients With COVID-19: Focus on Severity and Mortality

(2020) Jian-Min Jin et al.   Frontiers in Public Health

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

(2020) Bette Korber et al.   CELL

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

(2020) Erik Alm et al.   Eurosurveillance

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

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

(2020) Andrew Rambaut et al.   Nature Microbiology

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

(2020) Lucy van Dorp et al.   INFECTION GENETICS AND EVOLUTION

Stability of SARS-CoV-2 phylogenies

(2020) Yatish Turakhia et al.   PLoS Genetics

SnapperDB: a database solution for routine sequencing analysis of bacterial isolates

(2018) Timothy Dallman et al.   BIOINFORMATICS

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

(2017) Yuelong Shu et al.   Eurosurveillance

The International Nucleotide Sequence Database Collaboration

(2015) Guy Cochrane et al.   NUCLEIC ACIDS RESEARCH

Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences

(2012) Josephine Bryant et al.   Future Microbiology

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic

(2009) Gavin J. D. Smith et al.   NATURE