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XBB.1.16 sublineage with S:A27S and S:R408S substitutions #1894

Closed biome-datascientist closed 1 year ago

biome-datascientist commented 1 year ago

Description Sub-lineage of: XBB.1.16 Earliest sequence: 2023-01-09 Most recent sequence: 2023-04-04 Countries: India, Singapore, USA, Canada .... Query in CovSpectrum: XBB.1.16* (Nextclade) + S:R408S, S:A27S Substitutions in the background of XBB.1.16: S:A27S S:R408S

Additional mutations and its month wise frequency in India: Month_wise_mutations_calGISAID

Evidence: XBB 1 16+S_R408S

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3AR408S%2CS%3AA27S&nextcladePangoLineage=xbb.1.16*&

Escape calculator: bloom-408 https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/escape-calc/

Existing mutation spectrum in the spike gene of XBB.1.16:

XBB 1 16+S_R408S

https://outbreak.info/compare-lineages?pango=XBB.1.16&gene=S&threshold=75&nthresh=1&dark=false

Identified genomes:

EPI_ISL_17182905 EPI_ISL_17182925 EPI_ISL_17182930 EPI_ISL_17182931 EPI_ISL_17182934 EPI_ISL_17182949 EPI_ISL_17206426 EPI_ISL_17206435 EPI_ISL_17223627 EPI_ISL_17229374 EPI_ISL_17242420 EPI_ISL_17242422 EPI_ISL_17242423 EPI_ISL_17242424 EPI_ISL_17242438 EPI_ISL_17242439 EPI_ISL_17242440 EPI_ISL_17242441 EPI_ISL_17242442 EPI_ISL_17242443 EPI_ISL_17242445 EPI_ISL_17242446 EPI_ISL_17242447 EPI_ISL_17242448 EPI_ISL_17242450 EPI_ISL_17242451 EPI_ISL_17242452 EPI_ISL_17242453 EPI_ISL_17242458 EPI_ISL_17242473 EPI_ISL_17242479 EPI_ISL_17242480 EPI_ISL_17242497 EPI_ISL_17242503 EPI_ISL_17268903 EPI_ISL_17268904 EPI_ISL_17268909 EPI_ISL_17268910 EPI_ISL_17268916 EPI_ISL_17268917 EPI_ISL_17268925 EPI_ISL_17268929 EPI_ISL_17268930 EPI_ISL_17268945 EPI_ISL_17268956 EPI_ISL_17268957 EPI_ISL_17268958 EPI_ISL_17293132 EPI_ISL_17293133 EPI_ISL_17293134 EPI_ISL_17293136 EPI_ISL_17293137 EPI_ISL_17293138 EPI_ISL_17293140 EPI_ISL_17293141 EPI_ISL_17293142 EPI_ISL_17293146 EPI_ISL_17293148 EPI_ISL_17293152 EPI_ISL_17293153 EPI_ISL_17293157 EPI_ISL_17293159 EPI_ISL_17293161 EPI_ISL_17293162 EPI_ISL_17293163 EPI_ISL_17293169 EPI_ISL_17293171 EPI_ISL_17293173 EPI_ISL_17293174 EPI_ISL_17293177 EPI_ISL_17293178 EPI_ISL_17293181 EPI_ISL_17293184 EPI_ISL_17293185 EPI_ISL_17293186 EPI_ISL_17293187 EPI_ISL_17293189 EPI_ISL_17293190 EPI_ISL_17293193 EPI_ISL_17293195 EPI_ISL_17293196 EPI_ISL_17293197 EPI_ISL_17293198 EPI_ISL_17293203 EPI_ISL_17293219 EPI_ISL_17300662 EPI_ISL_17300782 EPI_ISL_17300783 EPI_ISL_17300785 EPI_ISL_17300792 EPI_ISL_17300795 EPI_ISL_17300796 EPI_ISL_17300798 EPI_ISL_17300801 EPI_ISL_17300821 EPI_ISL_17300827 EPI_ISL_17300834 EPI_ISL_17300836 EPI_ISL_17300837 EPI_ISL_17300851 EPI_ISL_17300858 EPI_ISL_17300860 EPI_ISL_17300862 EPI_ISL_17326864 EPI_ISL_17349533 EPI_ISL_17349539 EPI_ISL_17349543 EPI_ISL_17349561 EPI_ISL_17349588 EPI_ISL_17359471 EPI_ISL_17359472 EPI_ISL_17359476 EPI_ISL_17359485 EPI_ISL_17359490 EPI_ISL_17359492 EPI_ISL_17359508 EPI_ISL_17359510 EPI_ISL_17359526 EPI_ISL_17359532 EPI_ISL_17359534 EPI_ISL_17359542 EPI_ISL_17359547 EPI_ISL_17359548 EPI_ISL_17359549 EPI_ISL_17359550 EPI_ISL_17359553 EPI_ISL_17359554 EPI_ISL_17359555 EPI_ISL_17359556 EPI_ISL_17359557 EPI_ISL_17359558 EPI_ISL_17359559 EPI_ISL_17359560 EPI_ISL_17391177 EPI_ISL_17391186 EPI_ISL_17391188 EPI_ISL_17391189 EPI_ISL_17391191 EPI_ISL_17391192 EPI_ISL_17391193 EPI_ISL_17391206 EPI_ISL_17391207 EPI_ISL_17391374 EPI_ISL_17391380 EPI_ISL_17391381 EPI_ISL_17391403 EPI_ISL_17403724 EPI_ISL_17403726 EPI_ISL_17403727 EPI_ISL_17403728 EPI_ISL_17403731 EPI_ISL_17403734 EPI_ISL_17403736 EPI_ISL_17403737 EPI_ISL_17403740 EPI_ISL_17403744 EPI_ISL_17403752 EPI_ISL_17403753 EPI_ISL_17403754 EPI_ISL_17403762 EPI_ISL_17403765 EPI_ISL_17403767 EPI_ISL_17403768 EPI_ISL_17403769 EPI_ISL_17403770 EPI_ISL_17403773 EPI_ISL_17403774 EPI_ISL_17403778 EPI_ISL_17403779 EPI_ISL_17403780 EPI_ISL_17403781 EPI_ISL_17403785 EPI_ISL_17403788 EPI_ISL_17445676 EPI_ISL_17445677 EPI_ISL_17445678 EPI_ISL_17445680 EPI_ISL_17445684 EPI_ISL_17445685 EPI_ISL_17445686 EPI_ISL_17445687 EPI_ISL_17445690 EPI_ISL_17445691 EPI_ISL_17445695 EPI_ISL_17445699 EPI_ISL_17445700 EPI_ISL_17445702 EPI_ISL_17445703 EPI_ISL_17445706 EPI_ISL_17445707 EPI_ISL_17445709 EPI_ISL_17445727 EPI_ISL_17445728 EPI_ISL_17445733 EPI_ISL_17445736 EPI_ISL_17445737 EPI_ISL_17445739 EPI_ISL_17445740 EPI_ISL_17445741 EPI_ISL_17445744 EPI_ISL_17445747 EPI_ISL_17445762 EPI_ISL_17445763 EPI_ISL_17445766 EPI_ISL_17445770 EPI_ISL_17445774 EPI_ISL_17445779 EPI_ISL_17445782 EPI_ISL_17445786 EPI_ISL_17445790 EPI_ISL_17445793 EPI_ISL_17445798 EPI_ISL_17445800 EPI_ISL_17445802 EPI_ISL_17445804 EPI_ISL_17445806 EPI_ISL_17445814 EPI_ISL_17445815 EPI_ISL_17445816 EPI_ISL_17445837 EPI_ISL_17445841 EPI_ISL_17445842 EPI_ISL_17445845 EPI_ISL_17445846 EPI_ISL_17445849 EPI_ISL_17445850 EPI_ISL_17445854 EPI_ISL_17445855 EPI_ISL_17445857 EPI_ISL_17445858 EPI_ISL_17445859 EPI_ISL_17445860 EPI_ISL_17445861 EPI_ISL_17445862 EPI_ISL_17445863 EPI_ISL_17445864 EPI_ISL_17445865 EPI_ISL_17445866 EPI_ISL_17445867 EPI_ISL_17445868 EPI_ISL_17445869 EPI_ISL_17445870 EPI_ISL_17445871 EPI_ISL_17445873 EPI_ISL_17447210 EPI_ISL_17447215 EPI_ISL_17447216 EPI_ISL_17447217 EPI_ISL_17447219 EPI_ISL_17447222 EPI_ISL_17447223 EPI_ISL_17447225 EPI_ISL_17447227 EPI_ISL_17447229 EPI_ISL_17447230 EPI_ISL_17447233 EPI_ISL_17447236 EPI_ISL_17447240 EPI_ISL_17447249 EPI_ISL_17447252 EPI_ISL_17447253 EPI_ISL_17447255 EPI_ISL_17447256 EPI_ISL_17447259 EPI_ISL_17447268 EPI_ISL_17447271 EPI_ISL_17447279 EPI_ISL_17447280 EPI_ISL_17447287 EPI_ISL_17447288 EPI_ISL_17447289 EPI_ISL_17447298 EPI_ISL_17447303 EPI_ISL_17447312 EPI_ISL_17447316 EPI_ISL_17447328 EPI_ISL_17447332 EPI_ISL_17447336 EPI_ISL_17447341 EPI_ISL_17447357 EPI_ISL_17447370 EPI_ISL_17447371 EPI_ISL_17447372 EPI_ISL_17447388 EPI_ISL_17447390 EPI_ISL_17447391 EPI_ISL_17447399 EPI_ISL_17447400 EPI_ISL_17447401 EPI_ISL_17447402 EPI_ISL_17447404 EPI_ISL_17447406 EPI_ISL_17447409 EPI_ISL_17447410 EPI_ISL_17464043 EPI_ISL_17464044 EPI_ISL_17464046 EPI_ISL_17466156 EPI_ISL_17466157 EPI_ISL_17466158 EPI_ISL_17466159 EPI_ISL_17466160 EPI_ISL_17466161 EPI_ISL_17466162 EPI_ISL_17466164 EPI_ISL_17466165 EPI_ISL_17466166 EPI_ISL_17466168 EPI_ISL_17466169 EPI_ISL_17466170 EPI_ISL_17466171 EPI_ISL_17466172 EPI_ISL_17466173 EPI_ISL_17466174 EPI_ISL_17466175 EPI_ISL_17466176 EPI_ISL_17466177 EPI_ISL_17466178 EPI_ISL_17466179 EPI_ISL_17466374 EPI_ISL_17466375 EPI_ISL_17466376 EPI_ISL_17466377 EPI_ISL_17466381 EPI_ISL_17466382 EPI_ISL_17466383 EPI_ISL_17466384 EPI_ISL_17466385 EPI_ISL_17466386 EPI_ISL_17466387 EPI_ISL_17466388 EPI_ISL_17466389 EPI_ISL_17466390 EPI_ISL_17466392 EPI_ISL_17466393 EPI_ISL_17466394 EPI_ISL_17466396 EPI_ISL_17466397 EPI_ISL_17466898 EPI_ISL_17466902 EPI_ISL_17466906 EPI_ISL_17466909 EPI_ISL_17466910 EPI_ISL_17466913 EPI_ISL_17466915 EPI_ISL_17466916 EPI_ISL_17466917 EPI_ISL_17466921 EPI_ISL_17466927 EPI_ISL_17466928 EPI_ISL_17466931 EPI_ISL_17466961 EPI_ISL_17466964 EPI_ISL_17466976 EPI_ISL_17466978 EPI_ISL_17466986 EPI_ISL_17466991 EPI_ISL_17466996 EPI_ISL_17467004 EPI_ISL_17467023 EPI_ISL_17467033 EPI_ISL_17467034 EPI_ISL_17467038 EPI_ISL_17467047 EPI_ISL_17467051 EPI_ISL_17467057 EPI_ISL_17467058 EPI_ISL_17467067 EPI_ISL_17467098 EPI_ISL_17467100 EPI_ISL_17467109 EPI_ISL_17467114 EPI_ISL_17467115 EPI_ISL_17467118 EPI_ISL_17467119 EPI_ISL_17467122 EPI_ISL_17467124 EPI_ISL_17467125 EPI_ISL_17467131 EPI_ISL_17467136 EPI_ISL_17467139 EPI_ISL_17467146 EPI_ISL_17467148 EPI_ISL_17467154 EPI_ISL_17467157 EPI_ISL_17467184 EPI_ISL_17467196 EPI_ISL_17467197 EPI_ISL_17467208 EPI_ISL_17467218 EPI_ISL_17467228 EPI_ISL_17467240 EPI_ISL_17467257 EPI_ISL_17467278 EPI_ISL_17467293 EPI_ISL_17467300 EPI_ISL_17467305 EPI_ISL_17467308 EPI_ISL_17467312 EPI_ISL_17467314 EPI_ISL_17467316 EPI_ISL_17467336 EPI_ISL_17467344 EPI_ISL_17467352 EPI_ISL_17467358 EPI_ISL_17467363 EPI_ISL_17467364 EPI_ISL_17467369 EPI_ISL_17467373 EPI_ISL_17467377 EPI_ISL_17467378 EPI_ISL_17467380 EPI_ISL_17467381 EPI_ISL_17467386 EPI_ISL_17467387

Mutation map image source: https://covdb.stanford.edu/

aviczhl2 commented 1 year ago

S:A27S and S:R408S are defining mutations for XBB.1.16 on the current nextclade staging.

https://nextstrain.org/staging/nextclade/sars-cov-2/?label=clade:22F&s=XBB.1.16

aviczhl2 commented 1 year ago
Screen Shot 2023-04-15 at 14 07 01

Very few are having S:27A and 408R...

aviczhl2 commented 1 year ago

However usher seems to put every XBB.1.16 with S:27A. Is it a bug? @AngieHinrichs

Screen Shot 2023-04-15 at 14 09 08
AngieHinrichs commented 1 year ago

It is because of branch-specific masking. The BA.2 branch (which BTW has BA.4 and BA.5 as descendants) has several ranges including 21633-21641 masked (after sequences are added to the tree; branch-specific masking doesn't happen when sequences are uploaded to the web interface) because assembly errors often make false substitutions in the deleted regions.

Since XBB's parents are both BA.2 sublineages (BJ.1==BA.2.10.1.1 and BM.1.1.1==BA.2.75.3.1.1.1), I think XBB should have the BA.2 deletions, but I have not looked at the sequences.

corneliusroemer commented 1 year ago

408S is a common reversion to reference artefact