Section: Genomics
Topic: Genetics/Genomics, Health sciences, Microbiology

COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences

10.24072/pcjournal.333 - Peer Community Journal, Volume 3 (2023), article no. e101.

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Phylodynamic analyses can generate important and timely data to optimise public health response to SARS-CoV-2 outbreaks and epidemics. However, their implementation is hampered by the massive amount of sequence data and the difficulty to parameterise dedicated software packages. We introduce the COVFlow pipeline, accessible at https://gitlab.in2p3.fr/ete/CoV-flow, which allows a user to select sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database according to user-specified criteria, to perform basic phylogenetic analyses, and to produce an XML file to be run in the Beast2 software package. We illustrate the potential of this tool by studying two sets of sequences from the Delta variant in two French regions. This pipeline can facilitate the use of virus sequence data at the local level, for instance, to track the dynamics of a particular lineage or variant in a region of interest.  

Published online:
DOI: 10.24072/pcjournal.333
Type: Software tool
Keywords: COVID-19, molecular epidemiology, sequence database, phylogenetics, public health
Danesh, Gonché 1; Boennec, Corentin 1; Verdurme, Laura 2; Roussel, Mathilde 2; Trombert-Paolantoni, Sabine 2; Visseaux, Benoit 2; Haim-Boukobza, Stéphanie 2; Alizon, Samuel 1, 3

1 MIVEGEC, CNRS, IRD, Université de Montpellier, France
2 Laboratoire CERBA, Saint Ouen L’Aumône, France
3 Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
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     author = {Danesh, Gonch\'e and Boennec, Corentin and Verdurme, Laura and Roussel, Mathilde and Trombert-Paolantoni, Sabine and Visseaux, Benoit and Haim-Boukobza, St\'ephanie and Alizon, Samuel},
     title = {COVFlow: phylodynamics analyses of viruses from selected {SARS-CoV-2} genome sequences},
     journal = {Peer Community Journal},
     eid = {e101},
     publisher = {Peer Community In},
     volume = {3},
     year = {2023},
     doi = {10.24072/pcjournal.333},
     language = {en},
     url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.333/}
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Danesh, Gonché; Boennec, Corentin; Verdurme, Laura; Roussel, Mathilde; Trombert-Paolantoni, Sabine; Visseaux, Benoit; Haim-Boukobza, Stéphanie; Alizon, Samuel. COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences. Peer Community Journal, Volume 3 (2023), article  no. e101. doi : 10.24072/pcjournal.333. https://peercommunityjournal.org/articles/10.24072/pcjournal.333/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.genomics.100239

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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