Emergence of an early SARS-CoV-2 epidemic in the United States

[1]  M. Suchard,et al.  Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil , 2021, Science.

[2]  Gene W. Yeo,et al.  Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States , 2021, Cell.

[3]  M. Biggerstaff,et al.  Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021 , 2021, MMWR. Morbidity and mortality weekly report.

[4]  N. Loman,et al.  Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data , 2021, medRxiv.

[5]  Carl A. B. Pearson,et al.  Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England , 2021, Science.

[6]  Melis N. Anahtar,et al.  Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events , 2020, Science.

[7]  Jure Leskovec,et al.  Mobility network models of COVID-19 explain inequities and inform reopening , 2020, Nature.

[8]  Joel C. Miller,et al.  Superspreading events in the transmission dynamics of SARS-CoV-2: Opportunities for interventions and control , 2020, PLoS biology.

[9]  Joel O. Wertheim,et al.  The emergence of SARS-CoV-2 in Europe and North America , 2020, Science.

[10]  Joseph J. Sabia,et al.  The contagion externality of a superspreading event: The Sturgis Motorcycle Rally and COVID‐19 , 2020, Southern economic journal.

[11]  Melis N. Anahtar,et al.  Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events. , 2020, medRxiv.

[12]  E. Price-Haywood,et al.  Seroprevalence of SARS-CoV-2 and Infection Fatality Ratio, Orleans and Jefferson Parishes, Louisiana, USA, May 2020 , 2020, Emerging infectious diseases.

[13]  Edward C. Holmes,et al.  A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology , 2020, Nature Microbiology.

[14]  A. Vespignani,et al.  Estimating the establishment of local transmission and the cryptic phase of the COVID-19 pandemic in the USA , 2020, medRxiv.

[15]  S. Bhatt,et al.  Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe , 2020, Nature.

[16]  Trevor Bedford,et al.  Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California , 2020, Science.

[17]  M. Rieder,et al.  Evidence for Limited Early Spread of COVID-19 Within the United States, January–February 2020 , 2020, MMWR. Morbidity and mortality weekly report.

[18]  W. Hanage,et al.  Phylogenetic interpretation during outbreaks requires caution , 2020, Nature Microbiology.

[19]  Isaac I. Bogoch,et al.  Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States , 2020, Cell.

[20]  Matthew T. Maurano,et al.  Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City Region , 2020, medRxiv : the preprint server for health sciences.

[21]  Trevor Bedford,et al.  Cryptic transmission of SARS-CoV-2 in Washington state , 2020, Science.

[22]  Takuri Takahashi,et al.  Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak , 2020, Proceedings of the National Academy of Sciences.

[23]  Nuno R. Faria,et al.  The effect of human mobility and control measures on the COVID-19 epidemic in China , 2020, Science.

[24]  Anita Lerch,et al.  Estimating unobserved SARS-CoV-2 infections in the United States , 2020, Proceedings of the National Academy of Sciences.

[25]  Hannah R. Meredith,et al.  The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application , 2020, Annals of Internal Medicine.

[26]  E. Dong,et al.  An interactive web-based dashboard to track COVID-19 in real time , 2020, The Lancet Infectious Diseases.

[27]  Hannah R. Meredith,et al.  The incubation period of 2019-nCoV from publicly reported confirmed cases: estimation and application , 2020 .

[28]  E. Holmes,et al.  A new coronavirus associated with human respiratory disease in China , 2020, Nature.

[29]  Kai Zhao,et al.  A pneumonia outbreak associated with a new coronavirus of probable bat origin , 2020, Nature.

[30]  N. Linton,et al.  Real-Time Estimation of the Risk of Death from Novel Coronavirus (COVID-19) Infection: Inference Using Exported Cases , 2020, Journal of clinical medicine.

[31]  M. Santillana,et al.  Estimating the Early Outbreak Cumulative Incidence of COVID-19 in the United States: Three Complementary Approaches , 2020 .

[32]  Olga Chernomor,et al.  IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era , 2019, bioRxiv.

[33]  Daniel L. Ayres,et al.  BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics , 2019, Systematic biology.

[34]  P. Lemey,et al.  Tracking virus outbreaks in the twenty-first century , 2018, Nature Microbiology.

[35]  Karthik Gangavarapu,et al.  An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar , 2018, Genome Biology.

[36]  Daniel L. Ayres,et al.  Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 , 2018, Virus evolution.

[37]  Sven Rahmann,et al.  Genome analysis , 2022 .

[38]  Trevor Bedford,et al.  Nextstrain: real-time tracking of pathogen evolution , 2017, bioRxiv.

[39]  Trevor Bedford,et al.  Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples , 2017, Nature Protocols.

[40]  Jeffrey E. Barrick,et al.  Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. , 2014, Methods in molecular biology.

[41]  Heng Li.  Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[42]  Marc A Suchard,et al.  Three roads diverged? Routes to phylogeographic inference. , 2010, Trends in ecology & evolution.

[43]  Alexei J. Drummond,et al.  Bayesian Phylogeography Finds Its Roots , 2009, PLoS Comput. Biol..

[44]  Marco A. R. Ferreira,et al.  Bayesian analysis of elapsed times in continuous‐time Markov chains , 2008 .

[45]  Marc A Suchard,et al.  Counting labeled transitions in continuous-time Markov models of evolution , 2007, Journal of mathematical biology.

[46]  S. Ho,et al.  Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.

[47]  P. E. Kopp,et al.  Superspreading and the effect of individual variation on disease emergence , 2005, Nature.

[48]  H. Kishino,et al.  Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.