maybe typo "S:L452D" could be "S:L452R" + addition of B.1.1.519?

[tuspjo]

Dear Dr. Hodcroft,

I think there is a typo on this page https://covariants.org/variants/20A.S.478K "These sequences have Spike mutations at positions S:L452D (see Variant20C/S:452R page for more details) and MutationS:P681, both of which impact antibody binding."

I think it should be S:L452R, not S:L452D

Unrelated: the variant B.1.1.519 was first detected a week ago in my lab, and now we see it multiple times a day. Would you consider adding it to the mutation list? the variant seems to be most prevalent in Mexico and the US, and have these mutations (within my amplicon ;)) S:T478K, S:D614G, S:P681H, S:T732A, and one silent S:S691S (TCC->TCT)

Best

Tue

[patbohn]

"These sequences have Spike mutations at positions S:L452D (see Variant20C/S:452R page for more details) and MutationS:P681, both of which impact antibody binding."

Yes, I also just came across this, I believe it's in this file: https://github.com/hodcroftlab/covariants/blob/master/content/clusters/20A.S.154K.478K.md

[emmahodcroft]

Hi @tuspjo and @patbohn - thank you both! You're right, this should be 452R, not D. When typing these out it's not uncommon that I get the wrong amino acid as a typo, unfortunately! I appreciate your spotting it and letting me know :)

I've pushed this up to the preview site and should get it live very soon!

[emmahodcroft]

@patbohn Do you have a twitter account I can credit?

[emmahodcroft]

@tuspjo Is this the cluster you're referring to? https://nextstrain.org/groups/neherlab/ncov/S.P681?c=gt-S_478&label=mlabel:20B/A23756G

It certainly looks interesting, and has some international spread, but it is still fairly small compared to some variants of interest. I'm not sure I'd add it to CoVariants just yet, but if you keep me updated I would be happy to see if it might be added if it continues to grow?

I am curious though, I'll have a little look into it.

[emmahodcroft]

Here are the international and then by USA state that I find. I've got a focal build running now, will try to remember to push it up tomorrow and link it, if it works.

                 first_seq num_seqs    last_seq
USA             2020-11-01     8143  2021-04-28
Mexico          2020-11-13     3494  2021-04-22
Switzerland     2020-11-30      106  2021-04-22
Japan           2020-12-06        2  2020-12-28
United Kingdom  2020-12-12       18  2021-04-17
Canada          2020-12-18       32  2021-03-28
Kosovo          2020-12-27        1  2020-12-27
Costa Rica      2021-01-01        4  2021-03-08
Chile           2021-01-03        7  2021-04-08
Denmark         2021-01-04        9  2021-04-26
Luxembourg      2021-01-07        1  2021-01-07
Sweden          2021-01-09        3  2021-02-18
Israel          2021-01-10        6  2021-01-20
Brazil          2021-01-11        2  2021-01-28
Argentina       2021-01-14        1  2021-01-14
France          2021-01-15       37  2021-04-12
Spain           2021-01-15       34  2021-04-05
Germany         2021-01-18      189  2021-04-02
Aruba           2021-01-20       26  2021-04-06
New Zealand     2021-01-28        1  2021-01-28
Curacao         2021-02-08        7  2021-03-01
Netherlands     2021-02-10       39  2021-03-05
Italy           2021-02-11        1  2021-02-11
South Korea     2021-02-13        2  2021-02-16
Poland          2021-02-20        1  2021-02-20
Lithuania       2021-03-18        3  2021-03-21
Colombia        2021-03-29        1  2021-03-29
Australia       2021-04-26        3  2021-04-30

Ordered list by first_seq date:
                 first_seq num_seqs    last_seq
Washington DC   2020-11-01        6  2021-04-01
Arizona         2020-11-05      176  2021-04-15
Wyoming         2020-11-10       66  2021-04-23
Texas           2020-11-21      917  2021-04-23
Florida         2020-11-23      425  2021-04-16
Oregon          2020-11-23      118  2021-04-19
New York        2020-12-04      390  2021-04-28
California      2020-12-07     1204  2021-04-24
Indiana         2020-12-26      202  2021-04-16
Illinois        2020-12-27      311  2021-04-17
USA             2020-12-28        6  2021-04-01
Pennsylvania    2021-01-01      169  2021-04-14
Colorado        2021-01-03      234  2021-04-20
Michigan        2021-01-03      353  2021-04-14
Utah            2021-01-04       88  2021-04-15
West Virginia   2021-01-04       42  2021-04-06
Massachusetts   2021-01-06      116  2021-04-19
New Mexico      2021-01-07       70  2021-04-16
Georgia         2021-01-08       93  2021-04-14
Missouri        2021-01-09       79  2021-04-14
Maryland        2021-01-11      125  2021-04-06
New Jersey      2021-01-11      145  2021-04-15
Hawaii          2021-01-12       23  2021-04-02
Washington      2021-01-12      510  2021-04-25
Minnesota       2021-01-12      392  2021-04-19
Nebraska        2021-01-12       33  2021-04-17
Oklahoma        2021-01-13        8  2021-04-12
Iowa            2021-01-14       38  2021-04-08
Nevada          2021-01-14       66  2021-04-19
Kentucky        2021-01-15       38  2021-04-12
Louisiana       2021-01-17      143  2021-04-13
North Carolina  2021-01-18       88  2021-04-16
Puerto Rico     2021-01-18        9  2021-04-06
Ohio            2021-01-19      219  2021-04-15
Wisconsin       2021-01-20      310  2021-04-16
Kansas          2021-01-21      101  2021-04-21
Delaware        2021-01-22        7  2021-04-05
Virginia        2021-01-25       34  2021-04-10
Arkansas        2021-01-25       11  2021-04-11
Alabama         2021-01-26       19  2021-04-12
Rhode Island    2021-02-01       21  2021-04-14
North Dakota    2021-02-01       11  2021-03-28
Mississippi     2021-02-02       17  2021-04-08
Idaho           2021-02-02      101  2021-04-16
New Hampshire   2021-02-02       12  2021-04-21
Alaska          2021-02-04      460  2021-04-25
Connecticut     2021-02-08       35  2021-04-12
South Carolina  2021-02-10        6  2021-03-18
Maine           2021-02-21        4  2021-03-30
Montana         2021-02-22       26  2021-04-09
Tennessee       2021-02-25       51  2021-04-09
Vermont         2021-02-28        8  2021-04-01
South Dakota    2021-03-14        7  2021-04-04

[tuspjo]

Yes, that's it. The B.1.617.2 first found in India also carry the T478K, but several other mutations allows distinction of the B.1.617.2 and B.1.1.519.

Thank you!

[patbohn]

@patbohn Do you have a twitter account I can credit?

That'd be very kind, yes it's https://twitter.com/PatrickBohn13

Thank you!

[emmahodcroft]

No worries @patbohn ! :)

@tuspjo - here's the build ("S.732A" for the moment). Certainly a very distinct cluster, and some global spread (notable clusters in Germany, for example): https://nextstrain.org/groups/neherlab/ncov/S.732A

Zoomed to the cluster & coloured by country: https://nextstrain.org/groups/neherlab/ncov/S.732A?c=country&label=mlabel:20B/C203T&r=country

Do we know anything more about this variant? Are there any papers on it?

[emmahodcroft]

Also - apologies for the ignorance, but you said @tuspjo that you detected it a week ago in your lab - where is your lab - Denmark?

[tuspjo]

Yes. My lab does Sanger detection on a single amplicon bc it's dirt cheap&easy and can distinguish all known important variants, but it means that our data takes a bit to trickle through the various WGS pipelines before being deposited at GISAID, so Denmark is still listed as only having few B.1.1.519s. Currently, there's a confirmed outbreak of the B.1.1.519 here, so likely >100 WGS sequences will be coming the next weeks from Denmark, as all positive samples are WGSed.

[tuspjo]

I have not found much info on this variant, it's the dominating strain in Mexico, but only a few newspaper articles are mentioning it so far I think, and this preprint on T478K (which I think does not relate to the fact that the B.1.617.2 (Indian-2) also carries the T478K, maybe for timing reasons as B.1.617.2 is fairly recent): https://www.biorxiv.org/content/10.1101/2021.03.28.437369v3.full.pdf+html I think B.1.1.222 is a ancester of B.1.1.519, at least they share many mutations.