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robert-koch-institut / SARS-CoV-2-Sequenzdaten_aus_Deutschland

Ein zentraler Bestandteil einer erfolgreichen Erregersurveillance ist das Verständnis der Verbreitung eines Erregers sowie seiner pathogenen Eigenschaften. Hierbei stellt das Wissen über das Erregergenom eine wichtige Informationsquelle dar. So erlaubt der Nachweis von Mutationen im Genom eines Erregers, Verwandtschaftsbeziehungen zu rekonstruie...
https://robert-koch-institut.github.io/SARS-CoV-2-Sequenzdaten_aus_Deutschland/
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Very diverse set of sequences with S:P348H (almost exclusive to Germany) in just two submission dates #30

Closed corneliusroemer closed 2 months ago

corneliusroemer commented 2 years ago

I noticed that there are ~222 sequences from Germany with S:P384H that come from a big range of lineages suggesting the mutation is an artefact.

image image

Maybe this is a similar issue as in #27

Could you check with the lab what's going on there?

See where they lie on the tree - these are all the German ones, this mutation is basically non-existent outside of Germany

image

These are the EPI_ISLs: EPI_ISL_13241333 EPI_ISL_13241331 EPI_ISL_13944767 EPI_ISL_13241276 EPI_ISL_13241242 EPI_ISL_13944809 EPI_ISL_13241312 EPI_ISL_13944771 EPI_ISL_13944776 EPI_ISL_13241342 EPI_ISL_13944821 EPI_ISL_10294132 EPI_ISL_13241290 EPI_ISL_13944834 EPI_ISL_13944779 EPI_ISL_13241340 EPI_ISL_13944783 EPI_ISL_13241292 EPI_ISL_13241246 EPI_ISL_13241341 EPI_ISL_13944869 EPI_ISL_13241300 EPI_ISL_13944848 EPI_ISL_13241317 EPI_ISL_13241235 EPI_ISL_13944770 EPI_ISL_13241250 EPI_ISL_13241278 EPI_ISL_13241316 EPI_ISL_13241238 EPI_ISL_13241263 EPI_ISL_13241282 EPI_ISL_13241308 EPI_ISL_13241293 EPI_ISL_13944860 EPI_ISL_13944831 EPI_ISL_13241335 EPI_ISL_13944766 EPI_ISL_13241343 EPI_ISL_13944850 EPI_ISL_13241320 EPI_ISL_13241251 EPI_ISL_13944852 EPI_ISL_13944777 EPI_ISL_13241277 EPI_ISL_13241249 EPI_ISL_13241306 EPI_ISL_13241241 EPI_ISL_13241243 EPI_ISL_13241280 EPI_ISL_13944801 EPI_ISL_13241301 EPI_ISL_13944790 EPI_ISL_13944763 EPI_ISL_13944827 EPI_ISL_13944780 EPI_ISL_13944810 EPI_ISL_13944846 EPI_ISL_13241304 EPI_ISL_13241267 EPI_ISL_13944817 EPI_ISL_13944798 EPI_ISL_13944761 EPI_ISL_13241314 EPI_ISL_13241330 EPI_ISL_13944858 EPI_ISL_13944781 EPI_ISL_13944833 EPI_ISL_13241272 EPI_ISL_13241337 EPI_ISL_13241311 EPI_ISL_13241237 EPI_ISL_13241328 EPI_ISL_13241295 EPI_ISL_13944760 EPI_ISL_13944864 EPI_ISL_13241285 EPI_ISL_13944842 EPI_ISL_13944868 EPI_ISL_13944857 EPI_ISL_13241299 EPI_ISL_13944775 EPI_ISL_13241296 EPI_ISL_13944786 EPI_ISL_13944870 EPI_ISL_13241255 EPI_ISL_13944820 EPI_ISL_13944862 EPI_ISL_13944859 EPI_ISL_13241288 EPI_ISL_13944806 EPI_ISL_13241307 EPI_ISL_13241309 EPI_ISL_13944815 EPI_ISL_13241303 EPI_ISL_13241271 EPI_ISL_13241240 EPI_ISL_13944819 EPI_ISL_13944813 EPI_ISL_13944808 EPI_ISL_13241268 EPI_ISL_13944836 EPI_ISL_13241279 EPI_ISL_13944797 EPI_ISL_13241325 EPI_ISL_13944778 EPI_ISL_13944824 EPI_ISL_13944789 EPI_ISL_13944832 EPI_ISL_13241245 EPI_ISL_13944818 EPI_ISL_13944782 EPI_ISL_13241318 EPI_ISL_13944849 EPI_ISL_13944765 EPI_ISL_13944773 EPI_ISL_13241344 EPI_ISL_13944843 EPI_ISL_13241291 EPI_ISL_13944811 EPI_ISL_13241259 EPI_ISL_13944768 EPI_ISL_13944826 EPI_ISL_13944867 EPI_ISL_13944787 EPI_ISL_13241256 EPI_ISL_13241338 EPI_ISL_13944794 EPI_ISL_13944796 EPI_ISL_13241287 EPI_ISL_13944769 EPI_ISL_13944855 EPI_ISL_13241322 EPI_ISL_13241305 EPI_ISL_13241258 EPI_ISL_13241332 EPI_ISL_13241254 EPI_ISL_13241324 EPI_ISL_13241262 EPI_ISL_13944830 EPI_ISL_13944800 EPI_ISL_13944799 EPI_ISL_13944784 EPI_ISL_13944841 EPI_ISL_13241244 EPI_ISL_13944828 EPI_ISL_13944838 EPI_ISL_13944861 EPI_ISL_13241265 EPI_ISL_13944793 EPI_ISL_13944792 EPI_ISL_13241286 EPI_ISL_13241270 EPI_ISL_13241239 EPI_ISL_13241323 EPI_ISL_13241315 EPI_ISL_13241253 EPI_ISL_13944844 EPI_ISL_13944863 EPI_ISL_13944772 EPI_ISL_13944866 EPI_ISL_13241302 EPI_ISL_13241329 EPI_ISL_13944854 EPI_ISL_13241298 EPI_ISL_13241247 EPI_ISL_13241284 EPI_ISL_13944795 EPI_ISL_13944871 EPI_ISL_13944839 EPI_ISL_13944823 EPI_ISL_13241260 EPI_ISL_13944802 EPI_ISL_13944805 EPI_ISL_13944812 EPI_ISL_13944788 EPI_ISL_13944865 EPI_ISL_13241319 EPI_ISL_13241289 EPI_ISL_13241339 EPI_ISL_13944785 EPI_ISL_13241266 EPI_ISL_13944853 EPI_ISL_13944764 EPI_ISL_13241283 EPI_ISL_13241313 EPI_ISL_13241248 EPI_ISL_13944816 EPI_ISL_13241236 EPI_ISL_13944825 EPI_ISL_13944856 EPI_ISL_13944847 EPI_ISL_13944814 EPI_ISL_13241264 EPI_ISL_13241334 EPI_ISL_13944845 EPI_ISL_13241257 EPI_ISL_13241327 EPI_ISL_13241273 EPI_ISL_13241297 EPI_ISL_13944829 EPI_ISL_13241281 EPI_ISL_13944804 EPI_ISL_13241310 EPI_ISL_13944791 EPI_ISL_13944837 EPI_ISL_13241275 EPI_ISL_13944807 EPI_ISL_13944840 EPI_ISL_13241336 EPI_ISL_13944835 EPI_ISL_13241261 EPI_ISL_13241321 EPI_ISL_13944762 EPI_ISL_13944851 EPI_ISL_13944774 EPI_ISL_13944803 EPI_ISL_13944822 EPI_ISL_13241274 EPI_ISL_13241294 EPI_ISL_13241252 EPI_ISL_13241326

MarieLataretu commented 2 years ago

Hi @corneliusroemer , many thanks for reporting this!

Looking at the DESH data, it is most probably a (sequencing) lab bias. We are in contact with the lab.