Recent circulation of multiple sublineages of B.1.466.2 in Jakarta,Indonesia

[FedeGueli]

During the month of December 16 new sequences of B.1.466.2 have been sampled in Jakarta and West Java, clustering each one with different pre-delta Spring-Summer 2021 sequences.
In week 49-50-51 they represents between 1,5% and 2,5% of total sequences in Indonesia.
Obviously is too early to designate but i put them here to enable monitoring of them.

Lineage 1
EPI_ISL_8383532
with
Orf1a:F3644L
S:S1252F, ORF7b:D36G

Lineage 2
EPI_ISL_8383533, EPI_ISL_8383531
with
N:A35V
then
ORF1a:Q1021H, M3087I, ORF7b:S5L
then
Nuc:2740C
then
ORF1b:D2429G, S:T859I
then
S:A688S

Lineage 3
with
E: R61C
(EPI_ISL_8120473 adds:
ORF1a:V2149F, ORF1a:I3693V, ORF1a:E102K, Orf1a:A2355S, Orf1a:K3573E, Orf1b:A975V, Orf1b:A2431V
S: L249S, A475V, E484A, T572N, M: I82T, ORF6: I11T, ORF7a: A105V)
(EPI_ISL_8383540 adds: Orf1a:T4207I, ORF1a:K3353R, Orf1B:V1170F, ORF1a:M2374I, ORF8:W45L)
(EPI_ISL_8383553 adds: Orf1a:T4207I, ORF1a:A1352V, ORF1a:T4065I, S:L176F, ORF3a:T64I, 0RF3a:R122K)

Lineage 4
EPI_ISL_8383538, EPI_ISL_8383536, EPI_ISL_8383539
with
nuc: G17667A, C20703T
then
nuc: T18843C
then
nuc: G174C, ORF6:T21A
then
nuc: T10933C, ORF1b: M1596I, Orf1: G1772V

Lineage 5:
EPI_ISL_8131154
with :
Orf1b: M2667V
then
Orf1a:A4394T
then
ORF1a:S166G, G519S, A1679V, S2242F, T3082I, L3829F, Orf1b:D2090Y
S: T22I, N354D
M: I76V

Usher Tree

In the Jakarta metropolitan area these sequences represents around 10% in the last two weeks of December:

[MC240596]

I hope this isn't the next bad mutant

[FedeGueli]

@MC240596 i put this here just to monitor it, no reason to alarm or worries about it. Usually vocs have been anticipated by a raise in cases then linked to a variant. This is NOT the case.

you can check here

[AngieHinrichs]

Most of these sequences have very few differences with Indonesian sequences collected in May or June 2021... I wonder if the December sample collection dates are correct.

Lineage 1: Indonesia/JK-GS-FKUINIHRD-0293/2021|EPI_ISL_8383532|2021-12-25 seems to have the same mutations as Indonesia/KR-GS-FKUINIHRD-0089/2021|EPI_ISL_6959830|2021-06-05:
https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/pango-designation-405.lin1.json?branchLabel=Spike%20mutations&c=pango_lineage_usher&label=nuc%20mutations:A6015G,C12439T

Lineage 2: very similar to sequences from 2021-06-05 that already had S:T859I and S:A688S
https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/pango-designation-405.lin2.json?branchLabel=Spike%20mutations&c=pango_lineage_usher&label=nuc%20mutations:A20753G,C24138T

Lineage 3: Indonesia/JB-GS-WJHL-ITB-A112/2021|EPI_ISL_8120473|2021-12-06 has 15 private mutations relative to its most likely common ancestor with earlier sequences. The other two sequences are less diverged relative to samples from April/May/June.
https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/pango-designation-405.lin3.json?branchLabel=Spike%20mutations&c=pango_lineage_usher&label=nuc%20mutations:C26425T

Lineage 4: Three mutations relative to common ancestor with sequences from May/June:
https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/pango-designation-405.lin4.json?branchLabel=Spike%20mutations&c=pango_lineage_usher&label=nuc%20mutations:G17667A,C20703T

Lineage 5: Indonesia/JK-GS-GSILab-843004/2021|EPI_ISL_8131154|2021-12-20 has 27 private mutations relative to its most likely common ancestor with earlier sequences.
https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/pango-designation-405.lin5.json?branchLabel=Spike%20mutations&c=pango_lineage_usher&label=nuc%20mutations:A21466G,G28321A

[FedeGueli]

thx @AngieHinrichs , @c19270785 pointed that to me too.
Tough i think it is worth monitoring especially the most divergent ones. I put everything to describe the landscape in the best possible way.
Obviously if nothing more will emerge i'll close this issue.

[FedeGueli]

@thomaspeacock pointed to me that two more B.1.644.2 B.1.466.2 sequences popped up in indonesia

EPI_ISL_9702285
EPI_ISL_9242265

thx @corneliusroemer for the correction
 

[FedeGueli]

Two more B.1.466.2 sequences popped up in february.
EPI_ISL_10724195
EPI_ISL_10724194

It looks like that neither the january ones nor the february ones cluster with the ones described in this issue.
I dont know if such diversity comes from sequencing issues (last 4 have been sequenced by 3 different labs) or from low level circulation in different area of Indonesia ( last 4 seqs come from 3 different areas of the country)
@corneliusroemer

credits for these seqs @thomaspeacock

About B.1.466.2 i found this paper by Susanti et al:
https://www.biorxiv.org/content/10.1101/2021.07.06.451270v3

[cinswasti]

It looks like that neither the january ones nor the february ones cluster with the ones described in this issue. I dont know if such diversity comes from sequencing issues (last 4 have been sequenced by 3 different labs) or from low level circulation in different area of Indonesia ( last 4 seqs come from 3 different areas of the country) @corneliusroemer

@FedeGueli Thank you for flagging this, so we can monitor it as you said.
The last 3 were actually sequenced by the same lab (NIHRD), but samples originated from different labs/hospital. These 3 sequences were also ones with additional warning/comments in their sequencing metadata.

On the dozen or so came up in December, we are trying to liase with submitting labs to recheck the collection dates as @AngieHinrichs suggested.

[chrisruis]

Hi @cinswasti Have you had any luck with getting more information on the collection dates for these?

I'll put a monitor label on this for now

[cinswasti]

Hi @chrisruis, I'm afraid not yet. We are still liaising with the institutions to get permission to carry out data check.
The monitor label would be the best thing for now. Will keep this updated.

[chrisruis]

Thanks @cinswasti

[FedeGueli]

one more B.1.466.2 from March 2022 , Lampung region: EPI_ISL_12089943 with S:E484A and F490V
Please @cinswasti could you take a look at it?

[chrisruis]

Hi @cinswasti Did you have any luck getting the collection dates for these sequences?

[chrisruis]

I can only see 1 sequence with a collection date since the start of April 2022. It's possible that this is still circulating but will close for now and can reopen if more sequences appear

[FedeGueli]

Agree. No news from Indonesia. We will see in the next months if that diversity is still circulating.