BA.5.3.5 (S:R346T) with S:N185del,S:F186I, Orf1a:S2625F , Orf1b:P1664S, S:N460K and S:K444N emerged recently in South Africa 32 seqs (9 out of 31 with additional mutations: S:Y144del + NSP5_L75F)

[FedeGueli]

@RajLabn noticed that US airport surveillance found recently three BA.5.3.5 and being something unusual at this point, i decided to look into them. It was immediately evident that also BA.5.3.5 has walked the path of combo 444N/460K as many lineages in 2022. Interestingly they were acquired in the time elsewhere they were already declining or have disappeared.

So i decided to propose it to keep tracked things , also i think that differentiated evolution timing could pose some moderate threats with an hypothetical old variant better fitting in a new immunity scenario ( we already saw something similar with the Ba.2.75 comeback after BA.5 while BQ.1 was rising)

***IMPORTANT (EDITED): Back in January i proposed a sublineage of this one proposed here (issue #1566 )

The interesting thing i recalled seeing #1566 is that all the sequences of this proposed lineage carry an additional 3 nuc deletion between S:185-186:

That gives: S:N185del S:F186I (@thomaspeacock could you check it please?).

Checking with Covpsectrum just 27 BA.5.3.5 sequences had this S:N185-,S:f186I deletion, so this mean that it starts exactly at the start of the branch: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=S%3AF186I&nucMutations=C13252T&nextcladePangoLineage=BA.5.3.5*&aaMutations1=S%3A153I%2CS%3A1258Q%2CN%3A151L&

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Defining mutations: (EDITED accordingly at what i wrote just above) BA.5.3.5 > > >C1912T, Orf1b:P1664S (C18457T = NSP14_P140S), S:N185del , S:F186I (22116-22118del) then Orf1a:S2625F (C8139T = NSP3_S1807F) > C14925T > S:K444N (G22894T), S:N460K (T22942G)

Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_b7d7_ebda60.json?c=gt-nuc_1912&label=id:node_5788480

Gisaid Query: C18457T ,C1912T, C8139T, C14925T

Sequences: 29 EPI_ISL_16415539, EPI_ISL_16521179-16521180, EPI_ISL_16585491, EPI_ISL_16585493, EPI_ISL_16585496, EPI_ISL_16738358-16738363, EPI_ISL_16911595, EPI_ISL_17002108, EPI_ISL_17150205, EPI_ISL_17150207, EPI_ISL_17156142, EPI_ISL_17156351, EPI_ISL_17156353, EPI_ISL_17200356, EPI_ISL_17233121-17233122, EPI_ISL_17233239, EPI_ISL_17233242, EPI_ISL_17233247, EPI_ISL_17233254, EPI_ISL_17247149, EPI_ISL_17269457-17269458,

Interestingly the first sequence of this lineage we have is from an elderly women two days before Xmas 2022 in Cape Town.

Second point worth to be highlighted : 8 out of 29 sequences gained further S:144del : they are the branch starting with a notable NSP5 (MPro) mutation Orf1a:L3338F (C10277T= NSP5_L75F), T26624C, C7528T:

[FedeGueli]

This didnt spread further

[FedeGueli]

One more sequence of this came a couple of weeks ago. https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_31d21_b00750.json?label=id:node_7191630