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Diverse BA.2 and BA.5 sequences with spurious T11524C and A11537G -- primer trimming? #28

Closed AngieHinrichs closed 2 years ago

AngieHinrichs commented 2 years ago

I have noticed a pattern, almost exclusively in RKI sequences (but also in a few sequences from the Netherlands and France), of T11524C and A11537G occurring together in many different branches and sub-lineages of BA.2 and BA.5. It seems unlikely that those two mutations would co-occur dozens of times in sequences from many different lineages of BA.2 and BA.5. I collected some examples of what this looks like in a phylogenetic tree in a comment in cov-lineages/pango-designation#841. Then @JosetteSchoenma replied that this problem had been seen also in the Netherlands, but @JordyCoolen fixed it in https://github.com/JordyCoolen/easyseq_covid19/commit/e2412313ddaaf39a0b8014e4209d01c32a4d3245 by adjusting a primer trimming region to start at 11520 instead of 11525.

I am hopeful that a similar fix would remove the spurious T11524C + A11537G calls in so many RKI sequences. I don't have a list of affected sequences, but could make one if that would help. A few examples:

BA.5.1: Germany/NW-RKI-I-869542/2022 EPI_ISL_13382739 Germany/NI-RKI-I-869485/2022 EPI_ISL_13382683 Germany/NW-RKI-I-845428/2022 EPI_ISL_13239109

BA.5.2.1: Germany/NW-RKI-I-835345/2022 EPI_ISL_13033644 Germany/NW-RKI-I-848455/2022 EPI_ISL_13241301 Germany/NW-RKI-I-799266/2022 EPI_ISL_12739153

BA.5.3.2: Germany/SH-RKI-I-784836/2022 EPI_ISL_12674661 Germany/SH-RKI-I-823299/2022 EPI_ISL_13001607 Germany/NW-RKI-I-739643/2022 EPI_ISL_12346538

BA.2.36: Germany/BW-RKI-I-835322/2022 EPI_ISL_13033622 Germany/SN-RKI-I-723436/2022 EPI_ISL_12192631 Germany/NW-RKI-I-690722/2022 EPI_ISL_11818175

BA.2: Germany/BW-RKI-I-542774/2022 EPI_ISL_10032437 Germany/BW-RKI-I-542785/2022 EPI_ISL_10032456 Germany/NW-RKI-I-845418/2022 EPI_ISL_13239099

BA.2.9: Germany/NW-RKI-I-614789/2022 EPI_ISL_11455600 Germany/NW-RKI-I-637027/2022 EPI_ISL_11480485 Germany/NW-RKI-I-644150/2022 EPI_ISL_11591637

A11537G belongs in BA.1 -- but T11524C seems to occur independently many times in the BA.1 branches of the UCSC/UShER tree as well. So this probably affects all Omicron sequences.

Thanks!

AngieHinrichs commented 2 years ago

Not sure how this duplicate was created, closing.