We’ve prepared a short report on the early introductions and spread of #SARS-CoV-2 in the northern regions of France doi.org/10.1101/2020.0…. Find some key messages below. #COVID19 (1/9)
Several early introductions to France do not appear to have led to further spread likely due to effective contact tracing and isolation. (2/9)
Most sequences from France are spread out in the diversity of clade G (@GISAID nomenclature). This represents local circulation with possibly multiple introductions, and one export to Algeria. (3/9)
The current dataset (France + other parts of the world) is not sufficient for reliable phylogeographic inferences – from where the virus was introduced remains unclear. (4/9)
The earliest sequence in France in clade G isn’t the least divergent in the clade + no travel history. With the syndromic surveillance -> suggests local circulation in undocumented infections prior to the wave of COVID-19 cases in France. (5/9)
In light of the importance of infections without much symptoms in the spread of the virus in France, and as we get closer to the progressive deconfinement date, it will be key to track these infections in further testing and sequencing. (6/9)
Thanks to all groups that shared their sequences and groups that rapidly released their manuscripts (find in suppl. mat.), that enabled us to get a small global phylogeny accessible here tinyurl.com/ybnm4fu. Thanks a lot @GISAID and @nextstrain for awesome tools. (7/9)
Thanks @GambaroFabi, S.Behillil, @artemvvv, F.Donati, M.Albert, A.Alexandru, M.Vanpeene, M.Bizard, A.Brisebarre, M.Barbet, F.Derrar, S.van der Werf, V.Enouf. @institutpasteur, @Pasteur_Algerie. (8/9)
Phylogeny here considers early genomes, mostly France, w/ very little diversity, weak node support by nt subs -> so here we used a simple @GISAID nomenclature instead of the forward-looking, newly proposed nomenclature here doi.org/10.1101/2020.0…. (9/9)
the full link: nextstrain.org/community/Simo…
