Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events

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

(2020) Ensheng Dong et al.   LANCET INFECTIOUS DISEASES

Prevalence of SARS-CoV-2 Infection in Residents of a Large Homeless Shelter in Boston

(2020) Travis P. Baggett et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Epidemiology of Covid-19 in a Long-Term Care Facility in King County, Washington

(2020) Temet M. McMichael et al.   NEW ENGLAND JOURNAL OF MEDICINE

Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing

(2020) Luca Ferretti et al.   SCIENCE

Public Health Response to the Initiation and Spread of Pandemic COVID-19 in the United States, February 24–April 21, 2020

(2020) Anne Schuchat et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Presymptomatic Transmission of SARS-CoV-2 — Singapore, January 23–March 16, 2020

(2020) Wycliffe E. Wei et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

High SARS-CoV-2 Attack Rate Following Exposure at a Choir Practice — Skagit County, Washington, March 2020

(2020) Lea Hamner et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

High COVID-19 Attack Rate Among Attendees at Events at a Church — Arkansas, March 2020

(2020) Allison James et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

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

(2020) Bette Korber et al.   CELL

Presymptomatic Transmission of SARS-CoV-2 Amongst Residents and Staff at a Skilled Nursing Facility: Results of Real-Time PCR and Serologic Testing

(2020) Scott A Goldberg et al.   CLINICAL INFECTIOUS DISEASES

The emergence of SARS-CoV-2 in Europe and North America

(2020) Michael Worobey et al.   SCIENCE

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Unbiased Deep Sequencing of RNA Viruses from Clinical Samples

(2016) Christian B. Matranga et al.   Jove-Journal of Visualized Experiments

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone

(2015) Daniel J. Park et al.   CELL

popart: full-feature software for haplotype network construction

(2015) Jessica W. Leigh et al.   Methods in Ecology and Evolution

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS