search

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/
Creative Commons Attribution 4.0 International
67 stars 7 forks source link

Potential sequencing error: S:Q1054E showing up in just Germany on all sorts of lineages #32

Open corneliusroemer opened 2 years ago

corneliusroemer commented 2 years ago

Looking at recent German sequences, I noticed that S:Q1054E has suddenly popped up all over the tree - not just in one but in all sorts of lineages.

It has also never appeared outside of Germany. That's very indicative of a sequencing error / artefact.

Could you check with the lab? That'd be great

Unfortunately it appears that the actual lab doing the sequencing is not provided in the GISAID metadata - it seems that the originating lab is the lab that did the PCR not the lab that did the sequencing.

It may be more useful to have the lab that did the sequencing listed there - as in this case there are a handful of labs with this error - but I strongly suspect it's in fact only one lab that did the sequencing for all the submitters.

For the large amount of money German labs get for each sequence (is it still >200 EUR) one should expect good quality and no errors like this that should easily be identified if the sequencing lab ran their sequences through e.g. Nextclade.

This issue is similar to #27 #30

Here's a covSpectrum query: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3AQ1054E&

These are EPI_ISLs: EPI_ISL_14432551 EPI_ISL_14414119 EPI_ISL_14432663 EPI_ISL_14520784 EPI_ISL_14414320 EPI_ISL_14408625 EPI_ISL_14367877 EPI_ISL_14367902 EPI_ISL_14520547 EPI_ISL_14402843 EPI_ISL_14432225 EPI_ISL_14520809 EPI_ISL_14378924 EPI_ISL_13945683 EPI_ISL_14408267 EPI_ISL_14520827 EPI_ISL_14432063 EPI_ISL_13921602 EPI_ISL_14432642 EPI_ISL_14520545 EPI_ISL_14416139 EPI_ISL_14367888 EPI_ISL_14520746 EPI_ISL_14520772 EPI_ISL_13921663 EPI_ISL_14432249 EPI_ISL_14520757 EPI_ISL_14408704 EPI_ISL_13946392 EPI_ISL_13921585 EPI_ISL_14415977 EPI_ISL_14415045 EPI_ISL_14408443 EPI_ISL_13921433 EPI_ISL_14416174 EPI_ISL_14520697 EPI_ISL_14520665 EPI_ISL_14520885 EPI_ISL_14379121 EPI_ISL_14378915 EPI_ISL_14409100 EPI_ISL_14403138 EPI_ISL_13921644 EPI_ISL_14432584 EPI_ISL_14432580 EPI_ISL_14379009 EPI_ISL_14432590 EPI_ISL_14432684 EPI_ISL_13921591 EPI_ISL_14520666 EPI_ISL_14520922 EPI_ISL_14432325 EPI_ISL_13921819 EPI_ISL_14520852 EPI_ISL_14379110 EPI_ISL_14398549 EPI_ISL_14521363 EPI_ISL_14432662 EPI_ISL_14432546 EPI_ISL_14403055 EPI_ISL_14520995 EPI_ISL_14520695 EPI_ISL_14367770 EPI_ISL_14367986 EPI_ISL_14402716 EPI_ISL_14414415 EPI_ISL_14379012 EPI_ISL_14520517 EPI_ISL_14521016 EPI_ISL_14409031 EPI_ISL_14379015 EPI_ISL_14407921 EPI_ISL_14402891 EPI_ISL_14520905 EPI_ISL_14395507 EPI_ISL_14432162 EPI_ISL_14520751 EPI_ISL_14415985 EPI_ISL_14414742 EPI_ISL_14432634 EPI_ISL_14408455 EPI_ISL_14416181 EPI_ISL_14379207 EPI_ISL_14409109 EPI_ISL_14432688 EPI_ISL_14416249 EPI_ISL_13946281 EPI_ISL_14395504 EPI_ISL_14432613 EPI_ISL_14367878 EPI_ISL_14432257 EPI_ISL_14432310 EPI_ISL_14432534 EPI_ISL_14520561 EPI_ISL_13942426 EPI_ISL_14520918 EPI_ISL_14415940 EPI_ISL_14520834 EPI_ISL_13945685 EPI_ISL_14432630 EPI_ISL_14432184 EPI_ISL_14413973 EPI_ISL_14368232 EPI_ISL_14416216 EPI_ISL_13936037 EPI_ISL_13946427 EPI_ISL_14520926 EPI_ISL_14415733 EPI_ISL_14432576 EPI_ISL_14520720 EPI_ISL_14402345 EPI_ISL_14520768 EPI_ISL_14521133 EPI_ISL_14367803 EPI_ISL_14414821 EPI_ISL_14414254 EPI_ISL_13946390 EPI_ISL_14432658 EPI_ISL_14432552 EPI_ISL_14415944 EPI_ISL_14520851 EPI_ISL_13942371 EPI_ISL_14378986 EPI_ISL_14432635 EPI_ISL_14432449 EPI_ISL_14414390 EPI_ISL_13921310 EPI_ISL_14367662 EPI_ISL_13945843 EPI_ISL_14414940 EPI_ISL_14378983 EPI_ISL_14379135 EPI_ISL_14432531 EPI_ISL_14379142 EPI_ISL_14521169 EPI_ISL_14432618 EPI_ISL_14432665 EPI_ISL_14414321 EPI_ISL_14432255 EPI_ISL_14432562 EPI_ISL_14408562 EPI_ISL_13946435 EPI_ISL_14520753 EPI_ISL_14408615 EPI_ISL_14379021 EPI_ISL_13935996 EPI_ISL_13921631 EPI_ISL_14408824 EPI_ISL_14367983 EPI_ISL_14379019 EPI_ISL_14408468 EPI_ISL_13921641 EPI_ISL_14367753 EPI_ISL_14408658 EPI_ISL_14432294 EPI_ISL_14520807 EPI_ISL_14379162 EPI_ISL_14432636 EPI_ISL_14379076 EPI_ISL_14520657 EPI_ISL_14520850 EPI_ISL_14520715 EPI_ISL_14432647 EPI_ISL_14402383 EPI_ISL_14432573 EPI_ISL_14520701 EPI_ISL_14432489 EPI_ISL_14520536 EPI_ISL_14379061 EPI_ISL_14520719 EPI_ISL_14415402 EPI_ISL_13935999 EPI_ISL_14379118 EPI_ISL_14378987 EPI_ISL_14395460 EPI_ISL_14432461 EPI_ISL_13921686 EPI_ISL_14415861 EPI_ISL_14432664 EPI_ISL_14408469 EPI_ISL_14379069 EPI_ISL_13942286 EPI_ISL_14408701 EPI_ISL_14432351 EPI_ISL_13942085 EPI_ISL_14432416 EPI_ISL_14408921 EPI_ISL_14408440 EPI_ISL_14378944 EPI_ISL_14520766 EPI_ISL_13941967 EPI_ISL_14520869 EPI_ISL_14432569 EPI_ISL_14398631 EPI_ISL_14379068 EPI_ISL_14520659 EPI_ISL_14402886 EPI_ISL_14520788 EPI_ISL_14432446 EPI_ISL_14408661 EPI_ISL_14379130 EPI_ISL_14367875 EPI_ISL_14408138 EPI_ISL_14408174 EPI_ISL_14367735 EPI_ISL_14398360 EPI_ISL_13936051 EPI_ISL_13921518 EPI_ISL_14408300 EPI_ISL_14416113 EPI_ISL_14413999 EPI_ISL_14432570 EPI_ISL_14432440 EPI_ISL_14416211 EPI_ISL_14403051 EPI_ISL_14407946 EPI_ISL_14379050 EPI_ISL_14408302 EPI_ISL_14520676 EPI_ISL_14520765 EPI_ISL_13945660 EPI_ISL_14402214 EPI_ISL_14520762 EPI_ISL_14432648 EPI_ISL_13945867 EPI_ISL_13921776 EPI_ISL_14414238 EPI_ISL_14520813 EPI_ISL_14415936 EPI_ISL_14367957 EPI_ISL_14521595 EPI_ISL_14415947 EPI_ISL_14520868 EPI_ISL_14520823 EPI_ISL_14415034 EPI_ISL_14432652 EPI_ISL_14416069 EPI_ISL_14402852 EPI_ISL_14408384 EPI_ISL_14414606 EPI_ISL_14402953 EPI_ISL_14520781 EPI_ISL_14408914 EPI_ISL_14408402 EPI_ISL_14408359 EPI_ISL_14408213 EPI_ISL_14408631 EPI_ISL_13921612 EPI_ISL_14416185 EPI_ISL_14408295 EPI_ISL_14432568 EPI_ISL_14408628 EPI_ISL_14403002 EPI_ISL_13921464 EPI_ISL_14407937 EPI_ISL_14520906 EPI_ISL_14395980 EPI_ISL_14414945 EPI_ISL_14408618 EPI_ISL_14415660 EPI_ISL_14402616 EPI_ISL_13946508 EPI_ISL_14432418 EPI_ISL_14432285 EPI_ISL_14432176 EPI_ISL_14432448 EPI_ISL_14401772 EPI_ISL_14402845 EPI_ISL_14408268 EPI_ISL_14408348 EPI_ISL_14414400 EPI_ISL_13942405 EPI_ISL_14520692 EPI_ISL_14432082 EPI_ISL_14379056 EPI_ISL_14367742 EPI_ISL_14520806 EPI_ISL_14432213 EPI_ISL_14408133 EPI_ISL_14416175 EPI_ISL_14379036 EPI_ISL_14432393 EPI_ISL_14414732 EPI_ISL_14432686 EPI_ISL_13922240 EPI_ISL_14408362 EPI_ISL_14432343 EPI_ISL_14408650 EPI_ISL_14401755 EPI_ISL_14520528 EPI_ISL_14402998 EPI_ISL_14402297 EPI_ISL_14521095 EPI_ISL_14379077 EPI_ISL_14402222 EPI_ISL_14367757 EPI_ISL_14520522 EPI_ISL_14416228 EPI_ISL_13945808 EPI_ISL_14409039 EPI_ISL_13921637 EPI_ISL_14520544 EPI_ISL_14415088 EPI_ISL_13921646 EPI_ISL_14395040 EPI_ISL_14402688 EPI_ISL_14432091 EPI_ISL_13921554 EPI_ISL_14432471 EPI_ISL_13921825 EPI_ISL_14520748 EPI_ISL_14520726 EPI_ISL_14408835 EPI_ISL_14379140 EPI_ISL_14408698 EPI_ISL_13946474 EPI_ISL_14367646 EPI_ISL_14409154 EPI_ISL_14408575 EPI_ISL_14367754 EPI_ISL_14432593 EPI_ISL_14367681 EPI_ISL_14408676 EPI_ISL_14367873 EPI_ISL_14520760 EPI_ISL_13945886 EPI_ISL_14520898 EPI_ISL_14398192 EPI_ISL_14414215 EPI_ISL_14367713 EPI_ISL_14379072 EPI_ISL_14395860 EPI_ISL_13936179 EPI_ISL_14379101 EPI_ISL_13945715 EPI_ISL_14408696 EPI_ISL_14432317 EPI_ISL_14378958 EPI_ISL_14432693 EPI_ISL_14402968 EPI_ISL_14378891 EPI_ISL_14408655 EPI_ISL_14408369 EPI_ISL_14408866 EPI_ISL_13921565 EPI_ISL_14432510 EPI_ISL_13945842 EPI_ISL_14378996 EPI_ISL_14415642 EPI_ISL_14521253 EPI_ISL_14408274 EPI_ISL_14408132 EPI_ISL_14398234 EPI_ISL_14402940 EPI_ISL_14367764 EPI_ISL_14413981 EPI_ISL_14414334 EPI_ISL_14414843 EPI_ISL_14402878 EPI_ISL_14521102 EPI_ISL_14520824 EPI_ISL_14432521 EPI_ISL_14432425 EPI_ISL_14432453 EPI_ISL_14432695 EPI_ISL_14379043 EPI_ISL_14520538 EPI_ISL_14402725 EPI_ISL_14379073 EPI_ISL_13921584 EPI_ISL_14520840 EPI_ISL_14401992 EPI_ISL_14432560 EPI_ISL_14520754 EPI_ISL_14402613 EPI_ISL_14520796 EPI_ISL_14432683 EPI_ISL_14432666 EPI_ISL_13945723 EPI_ISL_13945664 EPI_ISL_14432604 EPI_ISL_14432256 EPI_ISL_14408897 EPI_ISL_13946332 EPI_ISL_14416027 EPI_ISL_14432639 EPI_ISL_14403079 EPI_ISL_14408684 EPI_ISL_14379198 EPI_ISL_14520888

MarieLataretu commented 1 year ago

Hi @corneliusroemer , thanks again for reporting!

Here, it also looks like a (sequencing) lab bias in the DESH data. We are in contact with the lab.