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BA.5.2 sublineage with ORF9b:D16G, C1627T, A27038G (572 seq. c. 20% of global BA.5) #657

Closed agamedilab closed 2 years ago

agamedilab commented 2 years ago

Proposal for a sublineage of BA.5

Earliest sequence: 2022-03-10 (South Africa)

Countries detected: mainly South Africa (58 %) but also Australia, Austria, Belgium, Botswana, Brazil, Canada, Denmark, France, Germany, Iceland, India, Israel, Italy, Netherlands, Norway, Singapore, Spain, United Kingdom, USA

Defining mutations: A28330G = ORF9b:D16G C1627T A27038G

This variant is defined by three substitutions (ORF9b:D16G, C1627T, A27038G) and was first detected in South Africa but has managed to spread to 19 other countries. Currently it forms one of the major clades of BA.5. representing c. 24% (338/1436) genomes.

Tis variant is a sublineage defined by Orf9b:D16G (#551) so these issue may have to be resolved first before this one is designated. Also under circumstances it may be adavantagous to define the sublineage by multiple markers. For this reason i reopened the issue.

The variant is distinct from the variants defined by N:E136D (#550), ORF1ab:Q556K (#550), ORF10:L37F (#621) and ORF1b:M1156I (#625), S:V1230A, ORF1a:P2685S, C2338T (#652) and S:T76I (#656).

pic2

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_20a2a_780d00.json?branchLabel=nuc%20mutations&c=gt-nuc_28330&label=nuc%20mutations:C27889T

More descending nodes contain aa mutations (ORF1ab:V7086F, V3858L) (#618):

pic1

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_20a2a_780d00.json?branchLabel=aa%20mutations&c=gt-nuc_28330&label=nuc%20mutations:C27889T

Growth advantage of BA.5+ A28330G, C1627T, A27038G vs. BA.5: vsBA5 https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?pangoLineage=BA.5*&nucMutations1=A28330G%2CC1627T%2CA27038G&pangoLineage1=BA.5*&analysisMode=CompareToBaseline&

Growth advantage of BA.5+ A28330G, C1627T, A27038G vs. BA.4: vsBA4 https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?pangoLineage=BA.4*&nucMutations1=A28330G%2CC1627T%2CA27038G&pangoLineage1=BA.5*&analysisMode=CompareToBaseline&

EPI_ISL_11207525, EPI_ISL_11207535, EPI_ISL_11621354, EPI_ISL_11763507, EPI_ISL_11763512, EPI_ISL_11763513, EPI_ISL_11763514, EPI_ISL_11763515, EPI_ISL_11763516, EPI_ISL_11763521, EPI_ISL_11763528, EPI_ISL_11763533, EPI_ISL_11763535, EPI_ISL_11773274, EPI_ISL_11825947, EPI_ISL_11867415, EPI_ISL_11903041, EPI_ISL_11903042, EPI_ISL_11903043, EPI_ISL_11903045, EPI_ISL_11903046, EPI_ISL_11903048, EPI_ISL_11903049, EPI_ISL_11903050, EPI_ISL_11903052, EPI_ISL_11903062, EPI_ISL_11903064, EPI_ISL_11903065, EPI_ISL_12006285, EPI_ISL_12012890, EPI_ISL_12012905, EPI_ISL_12012919, EPI_ISL_12029894, EPI_ISL_12097388, EPI_ISL_12097392, EPI_ISL_12097395, EPI_ISL_12097397, EPI_ISL_12097406, EPI_ISL_12097407, EPI_ISL_12097408, EPI_ISL_12097409, EPI_ISL_12097410, EPI_ISL_12207803, EPI_ISL_12243752, EPI_ISL_12267755, EPI_ISL_12267756, EPI_ISL_12267763, EPI_ISL_12268493, EPI_ISL_12268503, EPI_ISL_12268513, EPI_ISL_12273993, EPI_ISL_12274002, EPI_ISL_12278971, EPI_ISL_12278976, EPI_ISL_12278977, EPI_ISL_12278981, EPI_ISL_12278983, EPI_ISL_12278986, EPI_ISL_12278990, EPI_ISL_12278991, EPI_ISL_12278992, EPI_ISL_12278994, EPI_ISL_12278998, EPI_ISL_12291987, EPI_ISL_12292991, EPI_ISL_12293141, EPI_ISL_12293155, EPI_ISL_12293290, EPI_ISL_12307652, EPI_ISL_12307671, EPI_ISL_12307676, EPI_ISL_12342127, EPI_ISL_12401048, EPI_ISL_12401077, EPI_ISL_12401080, EPI_ISL_12401081, EPI_ISL_12401126, EPI_ISL_12401161, EPI_ISL_12401168, EPI_ISL_12401169, EPI_ISL_12401170, EPI_ISL_12401171, EPI_ISL_12406393, EPI_ISL_12426941, EPI_ISL_12431317, EPI_ISL_12439885, EPI_ISL_12456712, EPI_ISL_12472550, EPI_ISL_12473106, EPI_ISL_12473521, EPI_ISL_12473571, EPI_ISL_12473572, EPI_ISL_12473574, EPI_ISL_12473575, EPI_ISL_12473577, EPI_ISL_12473578, EPI_ISL_12473581, EPI_ISL_12473582, EPI_ISL_12473583, EPI_ISL_12473586, EPI_ISL_12473589, EPI_ISL_12473592, EPI_ISL_12473593, EPI_ISL_12473594, EPI_ISL_12473596, EPI_ISL_12473598, EPI_ISL_12473599, EPI_ISL_12473603, EPI_ISL_12473604, EPI_ISL_12473606, EPI_ISL_12473609, EPI_ISL_12473610, EPI_ISL_12473876, EPI_ISL_12474466, EPI_ISL_12474467, EPI_ISL_12474473, EPI_ISL_12474479, EPI_ISL_12477016, EPI_ISL_12477018, EPI_ISL_12477020, EPI_ISL_12477039, EPI_ISL_12489816, EPI_ISL_12492029, EPI_ISL_12495201, EPI_ISL_12511467, EPI_ISL_12511475, EPI_ISL_12511478, EPI_ISL_12511482, EPI_ISL_12511483, EPI_ISL_12519998, EPI_ISL_12534980, EPI_ISL_12557593, EPI_ISL_12557952, EPI_ISL_12558812, EPI_ISL_12559411, EPI_ISL_12559412, EPI_ISL_12559413, EPI_ISL_12559415, EPI_ISL_12559418, EPI_ISL_12559419, EPI_ISL_12559423, EPI_ISL_12559424, EPI_ISL_12559425, EPI_ISL_12559426, EPI_ISL_12559427, EPI_ISL_12559429, EPI_ISL_12559432, EPI_ISL_12559433, EPI_ISL_12559434, EPI_ISL_12559435, EPI_ISL_12559436, EPI_ISL_12559440, EPI_ISL_12559442, EPI_ISL_12559444, EPI_ISL_12559446, EPI_ISL_12559447, EPI_ISL_12559448, EPI_ISL_12559449, EPI_ISL_12561212, EPI_ISL_12562014, EPI_ISL_12563489, EPI_ISL_12570845, EPI_ISL_12570849, EPI_ISL_12576075, EPI_ISL_12576080, EPI_ISL_12585864, EPI_ISL_12585892, EPI_ISL_12587418, EPI_ISL_12587440, EPI_ISL_12588803, EPI_ISL_12589340, EPI_ISL_12589393, EPI_ISL_12589394, EPI_ISL_12589398, EPI_ISL_12589400, EPI_ISL_12589402, EPI_ISL_12589404, EPI_ISL_12589405, EPI_ISL_12589406, EPI_ISL_12590612, EPI_ISL_12607952, EPI_ISL_12607956, EPI_ISL_12607984, EPI_ISL_12607997, EPI_ISL_12607998, EPI_ISL_12608355, EPI_ISL_12610219, EPI_ISL_12610550, EPI_ISL_12610552, EPI_ISL_12610575, EPI_ISL_12610579, EPI_ISL_12610587, EPI_ISL_12610590, EPI_ISL_12611442, EPI_ISL_12624430, EPI_ISL_12624556, EPI_ISL_12624601, EPI_ISL_12628220, EPI_ISL_12628227, EPI_ISL_12632047, EPI_ISL_12632483, EPI_ISL_12632509, EPI_ISL_12632568, EPI_ISL_12633005, EPI_ISL_12633212, EPI_ISL_12636044, EPI_ISL_12636091, EPI_ISL_12637237, EPI_ISL_12644818, EPI_ISL_12648645, EPI_ISL_12648953, EPI_ISL_12649069, EPI_ISL_12651958, EPI_ISL_12652759, EPI_ISL_12652799, EPI_ISL_12653062, EPI_ISL_12673606, EPI_ISL_12676008, EPI_ISL_12676625, EPI_ISL_12677397, EPI_ISL_12677460, EPI_ISL_12677468, EPI_ISL_12677881, EPI_ISL_12678310, EPI_ISL_12679145, EPI_ISL_12688835, EPI_ISL_12694987, EPI_ISL_12694990, EPI_ISL_12694991, EPI_ISL_12694993, EPI_ISL_12694994, EPI_ISL_12694995, EPI_ISL_12694996, EPI_ISL_12694997, EPI_ISL_12694999, EPI_ISL_12695002, EPI_ISL_12695003, EPI_ISL_12695009, EPI_ISL_12695010, EPI_ISL_12695011, EPI_ISL_12695012, EPI_ISL_12695013, EPI_ISL_12695014, EPI_ISL_12695015, EPI_ISL_12695016, EPI_ISL_12695018, EPI_ISL_12695020, EPI_ISL_12695022, EPI_ISL_12695023, EPI_ISL_12695029, EPI_ISL_12696267, EPI_ISL_12698762, EPI_ISL_12698780, EPI_ISL_12699516, EPI_ISL_12699555, EPI_ISL_12699895, EPI_ISL_12701278, EPI_ISL_12704095, EPI_ISL_12705881, EPI_ISL_12705907, EPI_ISL_12705913, EPI_ISL_12705960, EPI_ISL_12705962, EPI_ISL_12705988, EPI_ISL_12705998, EPI_ISL_12706001, EPI_ISL_12706810, EPI_ISL_12707544, EPI_ISL_12707642, EPI_ISL_12708512, EPI_ISL_12708585, EPI_ISL_12708589, EPI_ISL_12709952, EPI_ISL_12711074, EPI_ISL_12713139, EPI_ISL_12713140, EPI_ISL_12713162, EPI_ISL_12713888, EPI_ISL_12715947, EPI_ISL_12720854, EPI_ISL_12720860, EPI_ISL_12720921, EPI_ISL_12724241, EPI_ISL_12726761, EPI_ISL_12726862, EPI_ISL_12728233, EPI_ISL_12728612, EPI_ISL_12728655, EPI_ISL_12730150, EPI_ISL_12733134, EPI_ISL_12734953, EPI_ISL_12735611, EPI_ISL_12735760, EPI_ISL_12736764, EPI_ISL_12736765, EPI_ISL_12736919, EPI_ISL_12737252, EPI_ISL_12737259, EPI_ISL_12737342, EPI_ISL_12737614, EPI_ISL_12739063, EPI_ISL_12739142, EPI_ISL_12739153, EPI_ISL_12740246, EPI_ISL_12740251, EPI_ISL_12741203, EPI_ISL_12741233, EPI_ISL_12741881, EPI_ISL_12742176, EPI_ISL_12745482, EPI_ISL_12751823, EPI_ISL_12752766, EPI_ISL_12759185, EPI_ISL_12761322, EPI_ISL_12763693, EPI_ISL_12763711, EPI_ISL_12763713, EPI_ISL_12763721, EPI_ISL_12763724, EPI_ISL_12763757, EPI_ISL_12763759, EPI_ISL_12763789, EPI_ISL_12763813, EPI_ISL_12763827, EPI_ISL_12765590, EPI_ISL_12765603, EPI_ISL_12765623, EPI_ISL_12765627, EPI_ISL_12765635, EPI_ISL_12765637, EPI_ISL_12767816, EPI_ISL_12767850, EPI_ISL_12768709, EPI_ISL_12769205, EPI_ISL_12769206, EPI_ISL_12769207, EPI_ISL_12769208, EPI_ISL_12769532

silcn commented 2 years ago

This is a sublineage of #551, as A28330G = ORF9b:D16G (note ORF9b overlaps with N)

agamedilab commented 2 years ago

you are right. i missed that A28330G = ORF9b:D16G probably because nextstrain apparently bugs out when coloring the branches by genotype, ORF9b, 16. I will best close that one.

FedeGueli commented 2 years ago

The sub-branch of this one with ORF1ab:V7086F, V3858L has been proposed in #618

So eventually the order is #551 #657 and then #618 @corneliusroemer @chrisruis

agamedilab commented 2 years ago

This variant is a sublineage of recently designated BA.5.2 defined by Orf9b:D16G (https://github.com/cov-lineages/pango-designation/issues/551). At the moment the variant BA.5 +ORF9b:D16G, C1627T, A27038G is similar but not equivalent to BA.5.2 (i.e. c. 21% of BA.5 +ORF9b:D16G do not carry C1627T, A27038G). Therefore i leave this post open for the case that further subdivision of BA.5.2 becomes necessary (e.g against the subclade defined by G12310A):

grafik

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_5099_462230.json?branchLabel=nuc%20mutations&c=gt-nuc_12310&label=nuc%20mutations:A28330G

InfrPopGen commented 2 years ago

Thanks for submitting. We've added lineage BA.5.2.1 with 201 newly designated sequences, and 125 updated designations. Defining mutation(s) C1627T and A27038G.

FedeGueli commented 2 years ago

I put here as a memorandum , cause maybe it could lead to some confusion or missassignment, there is also a BA.5 sublineage with C1627T without A28830G just 150 sequences but well spread in different countries Schermata 2022-06-04 alle 18 11 56

Here the usher link: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2da4d_b7e7e0.json?branchLabel=nuc%20mutations&c=country&label=nuc%20mutations:C1627T

Schermata 2022-06-04 alle 18 10 47

cc @AngieHinrichs i think the branch i mentioned is totally independent from BA.5.2.1 and real , but i would like a double check from you. Thanks!

AngieHinrichs commented 2 years ago

Thank you for pointing that out @FedeGueli. There are only 4 sequences to support the node with A28330G before C1627T, with the earliest date being SouthAfrica/CERI-KRISP-K039810/2022|EPI_ISL_12097388|2022-04-05, but the BA.5 > C1627T branch has more sequences and earlier dates like Eswatini/N40406/2022|EPI_ISL_12954170|2022-02-27 and Mauritius/N39598/2022|EPI_ISL_12954894|2022-03-09. Also, the current A28330G > C1627T branch has dates as early as SouthAfrica/CERI-KRISP-K037619/2022|EPI_ISL_11207525|2022-03-10.

So it seems more likely to me that C1627T should precede A28330G not vice versa. Am I missing some reason to think that A28330G before C1627T is correct? I think if I temporarily prune the four BA.5 samples with A28330G and not C1627T, and reoptimize the tree, then the tree will change to have BA.5 > C1627T > A28330G. And when the four samples are added back I expect they would just form a little BA.5 > A28330G branch.