Proposal for a potential sublineage of Lambda, with Spike L5F, L452Q, A475V, E484K, P499R, N501T, P681R (6 seqs, Peru)

[c19850727]

Description
Sub-lineage of: C.37
Earliest sequence: 2021/9/28
Most recent sequence: 2021/9/28
Countries circulating: Peru (Lambayeque region, in the Northern part of Peru)

Conserved substitutions:

Genomes:
EPI_ISL_5765587-5765588, EPI_ISL_5765597-5765598, EPI_ISL_5765604-5765605

Evidence:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_388e4_ca2d60.json?branchLabel=Spike%20mutations&c=gt-S_501,681&label=nuc%20mutations:C5893T,G7393A,C7712T,C9430T,C11124T,C16877T,C18395T,A20620G,A21488G,T21789C,C22267T,C22986T,G23012A,C23031T,C23058G,A23064C,C23525T,C23604G,C25207T,C26111A,G26199T,T26767C,T26894C

[georgimarinov]

Four sequences were posted from Arequipa with just N501T and with P681H:

EPI_ISL_6208676
EPI_ISL_6208675
EPI_ISL_6208674
EPI_ISL_5935407

[c19850727]

Yes.
It's interesting that small subclades with lots of substitutions now begin popping out across different part of Lambda tree, or is it because folks there begin sequencing more frequently?

[c19850727]

@georgimarinov It just popped out again...EPI_ISL_6574278.

[georgimarinov]

@georgimarinov It just popped out again...EPI_ISL_6574278.

As has another crazy version with R346S, G446S and E484V (EPI_ISL_6574198)

Also, there are now 16 sequences with both Q675H and Q677H, which seems to be another branch.

[chrisruis]

Thanks @c19850727 It looks like this clade still only has a few sequences in it currently so I'll add a monitor label for now and we can check back

[c19850727]

3 new sequences were just uploaded to GISAID, however they are all collected on September 29th (just one day after the initial 6 sequences) from the same region.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_18502_3ca0d0.json?branchLabel=aa%20mutations&c=gt-S_681&label=nuc%20mutations:C5893T,G7393A,C7712T,C9430T,C11124T,C16877T,C18395T,A20620G,A21488G,T21789C,C22267T,C22986T,G23012A,C23031T,C23058G,A23064C,C23525T,C23604G,C25207T,C26111A,G26199T,T26767C

[aineniamh]

Closing for now as is a stale issue.

[silcn]

A new extremely divergent sequence related to this cluster has just turned up: EPI_ISL_13915530. It is also from the Lambayeque region of Peru.

Shared spike mutations on top of Lambda: L5F, 68-71del, 144del, E484K, S490F (reversion), N501T, H655Y
Exclusive to the lineage in this issue: I76T (reversion), A475V, P499R, P681R
Exclusive to EPI_ISL_13915530: W64R, W152L, 210del, R346K, K417T, D420N, L441R, S477N, T478K, F486P, L727F, D950N

Would be interesting to know further details: in particular, which, if any, of the sequences were from chronic patients. The metadata from the new sequence doesn't match any of the September 2021 ones.
@Wen1953 @OrsonMM @Vjimenez-vasquez @LuisBarcenaF

https://nextstrain.org/fetch/github.com/silcn/subtreeAuspice1/raw/main/auspice/subtreeAuspice1_genome_2d09d_71d210.json?c=userOrOld&label=nuc%20mutations:C16877T,A21488G,G23012A,C23031T,A23064C,C23525T,C25207T,T26767C

[OrsonMM]

Hi @silcn

The genome was obtained from random surveillance and is not a chronic patient. Nevertheless, regions far from the capital (Lima) may be poorly represented in the time.

We are also keeping an eye on these rare cases of C.37, for example EPI_ISL_12590958 (2022-04-13 - Arequipa) and the genome you mention EPI_ISL_13915530. These have been the latest reports of C.37.

[FedeGueli]

Hi @silcn this one should not have S:681R, @ryhisner found it too and we discussed the absence of fcs mutation or maybe is it NNN?

[silcn]

@FedeGueli I think you must have misread my post? I list S:P681R as exclusive to the lineage in this issue (i.e. the one from September 2021) and not present in EPI_ISL_13915530. There are no NNNs in the spike, so it genuinely doesn't have an FCS mutation.

The 2nt mutation T23018C+T23019C = S:F486P, which goes via 486S or 486L, is starting to turn up increasingly often; it's also present in Constellation 1 from #844 and in a weird BA.2.10 from India uploaded yesterday (EPI_ISL_13929780) which also has W64R, 141-144del, 242-243del, F371S, G446S, R493Q, S494P, P1143L, and possibly even more because it has lots of NNNs.

S:L727F, which has never been seen before, is also a 2nt mutation (C23741T+A23743T). There's a silent mutation T23740C next to it too.

[FedeGueli]

oh sorry @silcn i misunderstood! yeah that Indian sequence found too by @ryhisner. agree it is popping up in very last days here and there. Thx

[shay671]

In the left are the unique mutations (not found in C.37) of the september clade. On the right of the May sample.
Many matches, in sites mainly of converges outside C.37.

Also- in the September clade and the may sample, the C.37 S:F490S
is missing. but in the September clade also the C.37 S:T76I is missing while it is present in the may sample.

[AngieHinrichs]

a 2nt mutation (C23741T+A23743T). There's a silent mutation T23740C next to it too.

FWIW when I see a single sample with multiple substitutions within a few bases of each other I'm a little suspicious because that's a pretty common error pattern (see "Neighbour linked variants" section of https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473/10). That's not to say it couldn't be real (like B.1.1's 28881-28883!), but error is my default assumption for that condition.