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

[1]  Ziheng Yang Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods , 1994, Journal of Molecular Evolution.

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

[3]  B. Rannala,et al.  Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference , 1996, Journal of Molecular Evolution.

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

[5]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[6]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[7]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[8]  Daniel L. Ayres,et al.  BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics , 2011, Systematic biology.

[9]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[10]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[11]  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.

[12]  Hayden C. Metsky,et al.  Genomic epidemiology reveals multiple introductions of Zika virus into the United States , 2017, Nature.

[13]  U. Obolski,et al.  Genomic and epidemiological monitoring of yellow fever virus transmission potential , 2018, Science.

[14]  M. Suchard,et al.  Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 , 2018, Systematic biology.

[15]  M. Kraemer,et al.  Reconstruction and prediction of viral disease epidemics , 2018, Epidemiology and Infection.

[16]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

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

[18]  Oliver G. Pybus,et al.  Precision epidemiology for infectious disease control , 2019, Nature Medicine.

[19]  Wenjun Ma,et al.  Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China , 2020, Cell.

[20]  M. Kuroda,et al.  A proposal of alternative primers for the ARTIC Network’s multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing , 2020, bioRxiv.

[21]  S. Mei,et al.  Evidence and characteristics of human-to-human transmission of SARS-CoV-2 , 2020, medRxiv.

[22]  Malik Peiris,et al.  Viral dynamics in mild and severe cases of COVID-19 , 2020, The Lancet Infectious Diseases.

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

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

[25]  G. Leung,et al.  First-wave COVID-19 transmissibility and severity in China outside Hubei after control measures, and second-wave scenario planning: a modelling impact assessment , 2020, The Lancet.

[26]  K. Yuen,et al.  Clinical Characteristics of Coronavirus Disease 2019 in China , 2020, The New England journal of medicine.

[27]  Ruifu Yang,et al.  An investigation of transmission control measures during the first 50 days of the COVID-19 epidemic in China , 2020, Science.

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