Potential new sublineage of B.1.617.2 with Spike A684S in Canada

[c19850727]

Potential sublineage of B.1.617.2 (25 sequences in Alberta, Canada) Earliest sequence: 2020/8/4 Most recent sequence: 2021/8/10 Mutations in addition to B.1.617.2: M: A81S N: S412R ORF1a: A687V, H712Q, V1550F, P1640L, A3209V, V3718A, T3750I ORF1b: M1499I ORF8: 119/120del ORF9b: M8T S: A222V, Q613H, A684S Genomes: EPI_ISL_3524943, EPI_ISL_3524970-3524971, EPI_ISL_3524986, EPI_ISL_3525009, EPI_ISL_3525019, EPI_ISL_3525156, EPI_ISL_3525186, EPI_ISL_3525193, EPI_ISL_3525204, EPI_ISL_3525211, EPI_ISL_3525219, EPI_ISL_3525230-3525231, EPI_ISL_3525239, EPI_ISL_3525304, EPI_ISL_3525399, EPI_ISL_3525406, EPI_ISL_3525412, EPI_ISL_3525414, EPI_ISL_3525418-3525419, EPI_ISL_3525435, EPI_ISL_3525440, EPI_ISL_3525453

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_4c5ca_1edef0.json

[babarlelephant]

Hi, does it deserve a lineage? I don't think A684S is concerning, it seems deleterious and would be able to propagate a bit more thanks to P681H/R.

From what I checked the 500 sequences usher subtree you are showing (lineage Delta+A222V+ T11938C,A14475G,G29422T) may represent 1/50th of the Delta+A222V lineage, itself being about 1/12th of Delta.

and all but 3 of the >500 sequences of this Delta+A222V+ T11938C,A14475G,G29422T lineage are from Canada.

To check the already assigned AY.x lineages, I computed a consensus of each lineage from lineages.csv and I obtained an usher tree showing that the T11938C sublineage of Delta+A2222V is not assigned yet.

[FedeGueli]

Michael Edwards brought to my attention this growing Delta sublineage in Sri Lanka carrying two spike mutations: S:A222V, A701S Here the nexstrain build https://nextstrain.org/community/aicbu/ncov/srilanka?c=gt-S_222,701&m=div

I would ask to @babarlelephant if it could have some relevance as we are not technical, before opening a new issue on it.

[babarlelephant]

@FedeGueli According to this tree whose root is at the root of the Delta+A222V lineage, the branch with C331T (say India, April) splits into a USA lineage and your almost purely Sri Lanka lineage (the one with S:A1078S). Some of these Sri Lanka sequences are designated as B.1.617.2 in lineages.csv.

[chrisruis]

Hi @FedeGueli, we're currently designating AY lineages that are epidemiologically distinct to enable fine-scale virus tracking (outlined at https://www.pango.network/new-ay-lineages/ and https://twitter.com/arambaut/status/1428272566469279749 if you haven't already seen them). So this Sri Lanka lineage looks like an ideal candidate for a new AY. Don't worry about submitting an issue for this one - I'll take a look at it and put the issue in tagging you if it all looks ok. Thanks!

[FedeGueli]

Thank you very much @chrisruis , So i opened a new issue #199 on this sublineage: https://github.com/cov-lineages/pango-designation/issues/199

Thank you @babarlelephant very much for your time.

[chrisruis]

Thanks @FedeGueli

[c19850727]

Hi, does it deserve a lineage? I don't think A684S is concerning, it seems deleterious and would be able to propagate a bit more thanks to P681H/R.

From what I checked the 500 sequences usher subtree you are showing (lineage Delta+A222V+ T11938C,A14475G,G29422T) may represent 1/50th of the Delta+A222V lineage, itself being about 1/12th of Delta.

and all but 3 of the >500 sequences of this Delta+A222V+ T11938C,A14475G,G29422T lineage are from Canada.

To check the already assigned AY.x lineages, I computed a consensus of each lineage from lineages.csv and I obtained an usher tree showing that the T11938C sublineage of Delta+A2222V is not assigned yet.

Hi Babar I think you are right.

I was a bit shocked at the first sight of so many A684S suddenly emerging in August in a few different clusters so I didn't check it before submitting...thanks for the reply and sorry for being dramatic.

[chrisruis]

Thanks @c19850727. As outlined here, we're designating AY lineages that are epidemiologically distinct. It's not clear that the clade that you proposed is epidemiologically distinct. However, it is part of a larger clade of sequences from Canada that is the result of one or more introductions into Canada with onward transmission. This larger clade does warrant a new AY lineage and we've added this as AY.27 in v1.2.68

We've started AY.27 on a branch with G29422T (synonymous) and it has 1092 sequence designations in v1.2.68: AY.27_sequences.txt

[corneliusroemer]

I stumbled across this issue when looking into S:613H homoplasies.

This is what AY.27 looks like in Canada at the moment (blue and green), the top is with S:613H in addition.

Unfortunately, pango-learn doesn't seem to designate any AY.27 at all. So it doesn't show up in outbreak.info or cov-spectrum.

[AngieHinrichs]

Unfortunately, pango-learn doesn't seem to designate any AY.27 at all. So it doesn't show up in outbreak.info or cov-spectrum.

@corneliusroemer Thanks so much for reporting that! I believe @rmcolq has fixed that in today's pangoLEARN release 2021-09-17. Hopefully that will be reflected in GISAID and outbreak.info soon (few days?).

[FedeGueli]

Hi all of you, following the great work of @corneliusroemer on it i was noticing that the Delta+613H is becoming a thing in Canada ( and not only there)

My main concern came from Alberta where it is increasing in frequency

And in Alberta the epidemiological situation is out of control: https://twitter.com/JenLeeCBC/status/1440382836431679489?s=20

I am not sure that there is any correlation between the two things but i hope professors @AngieHinrichs @chrisruis @rambaut @rmcolq @aineniamh could take a second look at this situation.

link of the screenshots Covid Spectrum https://cov-spectrum.ethz.ch/explore/Canada/AllSamples/AllTimes/variants/json=%7B%22variant%22%3A%7B%22name%22%3A%22B.1.617.2%22%2C%22mutations%22%3A[%22S%3AQ613H%22]%7D%2C%22matchPercentage%22%3A1%7D

Outbreak https://outbreak.info/situation-reports?pango&muts=S%3AQ613H&loc=USA&loc=USA_US-CA&loc=CAN&loc=DNK&selected=CAN&overlay=false

[silcn]

If anything S:Q613H has been stable at around 40% prevalence in Alberta since late July, which I would not call "increasing in frequency". CovSPECTRUM can produce unreliable estimates of transmissibility advantage when the increase in prevalence is due to a founder effect rather than a difference in fitness.

[FedeGueli]

If anything S:Q613H has been stable at around 40% prevalence in Alberta since late July, which I would not call "increasing in frequency". CovSPECTRUM can produce unreliable estimates of transmissibility advantage when the increase in prevalence is due to a founder effect rather than a difference in fitness.

i know well i didnt look at growth advantage, but at the epidemiological situation. there is not just trasmission advantage as possible issue.

[FedeGueli]

At the moment Alberta is experiencing the highest ratio icu per million pop, (between the countries on ourworldindata) despite 74% of fully vaxxed, and no age of vaccinated abnormality as we have seen in FLA or elsewhere.