
Evolutionary Biology
Early phylodynamics analysis of the COVID-19 epidemic in France
10.24072/pcjournal.40 - Peer Community Journal, Volume 1 (2021), article no. e45.
Get full text PDF Peer reviewed and recommended by PCIAuthor's affiliations:
@article{10_24072_pcjournal_40, author = {Danesh, Gonch\'e and Elie, Baptiste and Michalakis, Yannis and Sofonea, Mircea T and Bal, Antonin and Behillil, Sylvie and Destras, Gr\'egory and Boutolleau, David and Burrel, Sonia and Marcelin, Anne-Genevi\`eve and Plantier, Jean-Christophe and Thibault, Vincent and Simon-Loriere, Etienne and van der Werf, Sylvie and Lina, Bruno and Josset, Laurence and Enouf, Vincent and Alizon, Samuel}, title = {Early phylodynamics analysis of the {COVID-19} epidemic in {France}}, journal = {Peer Community Journal}, eid = {e45}, publisher = {Peer Community In}, volume = {1}, year = {2021}, doi = {10.24072/pcjournal.40}, url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.40/} }
TY - JOUR TI - Early phylodynamics analysis of the COVID-19 epidemic in France JO - Peer Community Journal PY - 2021 DA - 2021/// VL - 1 PB - Peer Community In UR - https://peercommunityjournal.org/articles/10.24072/pcjournal.40/ UR - https://doi.org/10.24072/pcjournal.40 DO - 10.24072/pcjournal.40 ID - 10_24072_pcjournal_40 ER -
Danesh, Gonché; Elie, Baptiste; Michalakis, Yannis; Sofonea, Mircea T; Bal, Antonin; Behillil, Sylvie; Destras, Grégory; Boutolleau, David; Burrel, Sonia; Marcelin, Anne-Geneviève; Plantier, Jean-Christophe; Thibault, Vincent; Simon-Loriere, Etienne; van der Werf, Sylvie; Lina, Bruno; Josset, Laurence; Enouf, Vincent; Alizon, Samuel. Early phylodynamics analysis of the COVID-19 epidemic in France. Peer Community Journal, Volume 1 (2021), article no. e45. doi : 10.24072/pcjournal.40. https://peercommunityjournal.org/articles/10.24072/pcjournal.40/
Peer reviewed and recommended by PCI : 10.24072/pci.evolbiol.100107
[1] The proximal origin of SARS-CoV-2, Nature Medicine, Volume 26 (2020) no. 4, pp. 450-452 | Article
[2] BEAST 2: A Software Platform for Bayesian Evolutionary Analysis, PLoS Computational Biology, Volume 10 no. 4 | Article
[3] Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data, Genetics, Volume 161 (2002), pp. 1307-1320
[4] Bayesian Phylogenetics with BEAUti and the BEAST 1.7, Molecular Biology and Evolution, Volume 29 (2012) no. 8, pp. 1969-1973 | Article
[5] Temporal signal and the phylodynamic threshold of SARS-CoV-2, Virus Evolution, Volume 6 (2020) no. 2 | Article
[6] Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing, Science, Volume 368 (2020) | Article
[7] Eight challenges in phylodynamic inference, Epidemics, Volume 10 (2015), pp. 88-92 | Article
[8] Introductions and early spread of SARS-CoV-2 in France, 24 January to 23 March 2020, Eurosurveillance, Volume 25 (2020) no. 26 | Article
[9] Unifying the Epidemiological and Evolutionary Dynamics of Pathogens, Science, Volume 303 (2004) no. 5656, pp. 327-332 | Article
[10] A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, Volume 52 (2003) no. 5, pp. 696-704 | Article
[11] Nextstrain: real-time tracking of pathogen evolution, Bioinformatics, Volume 34 (2018) no. 23, pp. 4121-4123 | Article
[12] The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2, Nature Microbiology, Volume 5 (2020) no. 4, pp. 536-544 | Article
[13] Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model, Journal of The Royal Society Interface, Volume 11 (2014) no. 94 | Article
[14] SMS: Smart Model Selection in PhyML, Molecular Biology and Evolution, Volume 34 (2017) no. 9, pp. 2422-2424 | Article
[15] Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia, New England Journal of Medicine, Volume 382 (2020) no. 13, pp. 1199-1207 | Article
[16] Secondary attack rate and superspreading events for SARS-CoV-2, The Lancet, Volume 395 (2020) no. 10227 | Article
[17] RDP4: Detection and analysis of recombination patterns in virus genomes, Virus Evolution, Volume 1 (2015) no. 1 | Article
[18] Phylodynamic Analysis | 176 genomes | 6 Mar 2020. en-US. http: //virological.org/t/phylodynamic-analysis-176-genomes-6-mar-2020/356 (visited on 04/26/2020), (2020)
[19] A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology, Nature Microbiology, Volume 5 (2020) no. 11, pp. 1403-1407 | Article
[20] Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen), Virus Evolution, Volume 2 (2016) no. 1 | Article
[21] Estimating the burden of SARS-CoV-2 in France, Science, Volume 369 (2020) no. 6500, pp. 208-211 | Article
[22] Phylodynamic analyses based on 93 genomes. file:///Users/bourguet/Downloads/2020-02-25%20report%20ScireVaughanStadler.pdf, 2020
[23] A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times, Bioinformatics, Volume 18 (2002) no. 1, pp. 115-123 | Article
[24] Memory is key in capturing COVID-19 epidemiological dynamics, Epidemics, Volume 35 (2021) | Article
[25] Estimating the Basic Reproductive Number from Viral Sequence Data, Molecular Biology and Evolution, Volume 29 (2012) no. 1, pp. 347-357 | Article
[26] Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV), Proceedings of the National Academy of Sciences, Volume 110 (2013) no. 1, pp. 228-233 | Article
[27] Fast Dating Using Least-Squares Criteria and Algorithms, Systematic Biology, Volume 65 (2015) no. 1, pp. 82-97 | Article
[28] Viral Phylodynamics, PLoS Computational Biology, Volume 9 (2013) no. 3 | Article
[29] Report 5: Phylogenetic analysis of SARS-CoV-2, (2020) | Article
[30] How generation intervals shape the relationship between growth rates and reproductive numbers, Proceedings of the Royal Society B: Biological Sciences, Volume 274 (2006) no. 1609, pp. 599-604 | Article
[31] A new coronavirus associated with human respiratory disease in China, Nature, Volume 579 (2020) no. 7798, pp. 265-269 | Article
[32] Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins, Nature, Volume 583 (2020) no. 7815, pp. 286-289 | Article
[33] A pneumonia outbreak associated with a new coronavirus of probable bat origin, Nature, Volume 579 (2020) no. 7798, pp. 270-273 | Article
Cited by Sources: