mpxv-lineages / lineage-designation Goto Github PK

Right now after every commit there's an autoupdate of the time stamp - this is very noisy. Would be good if the auto-update was only done when necessary.

There is a relatively large branch on the B.1 polytomy defined by the SNP C25644T.

It has at least 40 sequences in Genbank from a variety of countries including Germany, the UK, the US, Portugal, Mexico.

https://nextstrain.org/monkeypox/hmpxv1?c=gt-nuc_25644&m=div

It could be that this mutation has arisen another time on a different branch, as in the current Nextstrain tree the tree builder seems to place part of this lineage on a separate branch with G63147A

It's not clear to me whether C25644T is homoplasic and/or G63147A is homoplasic. IQtree sometimes put things one way, sometimes another.

https://nextstrain.org/monkeypox/hmpxv1?c=gt-nuc_25644,63147&m=div

Hello, everyone. Cases have been dropping, but we continue sequencing at INSColombia.
I see two likely B.1 sublineages with unique mutations related to cases in Colombia. I would find a designation useful to describe their circulation appropriately and continue surveillance. I appreciate your great work and thank any comments.

G161797A (Colombia)
https://nextstrain.org/staging/monkeypox/hmpxv1/?gt=nuc.161797A&m=div

G149818A (Germany,Colombia)
https://nextstrain.org/staging/monkeypox/hmpxv1/?gt=nuc.149818A&m=div

In the recent upload of sequences the's a new cluster that crosses the lineage definition threshold, defined by G181367A.

This cluster is mostly Portuguese so far - one sequence is from Canada.

There's another cluster of 2 sequences in A.2, similar to A.2.1 and A.2.2:

https://nextstrain.org/staging/monkeypox/hmpxv1/big?m=div

I propose to designate this as A.2.3

Defining mutations:
Unique: G2752A, C57284T, C74226T, G118739A, C146223T, G170317A, G172527A, C175759T, G189417A, C189474T
Homoplasies: G39173A, G61844A, G148427A, G150800A, G168365A

Sequences: ON676707, OP555515

There's a global B.1 sublineage with C182950T and 19 sequences to date.

It's been sequenced in a lot of countries, including once in Brazil and Colombia - which supports designation as there are not many public sequences from Brazil, so it is possible there are many more of this lineage than we know.

https://nextstrain.org/staging/monkeypox/hmpxv1/big?c=gt-nuc_182950&m=div

With the recent upload of another A.2 sequence from US-PA, there's a new cluster in A.2 that may deserve a designation to be able to talk about this cluster.

https://nextstrain.org/monkeypox/hmpxv1/2022-09-22?c=gt-nuc_67611,130231,159277&label=id:141ea44c&m=div

Lots of defining mutations (~20):
G11948A, C14790T, G21991A, G23118A, G38923A, G39515A, G56546A, G57786A, G93312A, C103019T, C112470T, C124129T, G135303A, G145902A, C149365T, G158424A, G162640A, G186984A, C127906T, G155611A

Outside of the 2022 outbreak lineage B.1, this year has seen around a dozen of submissions from clade A.2 - roughly a percent of this year's sequences.

There's a cluster of 4 sequences in A.2 that may be worth designating due to the likely under sampled nature of the A.2 lineage.

There are 4 sequences in this cluster (the two Indian sequences have been resequenced from culture, I'm not counting them here)

2 of these sequences, the Florida and UK ones are on Genbank, the Indian sequences are on GISAID.

Lineage defining mutations are:

C25072T
G36898A
G42183A
C42903T
G50346A
C54268T
G79406A
G105746A
A140492C
C142498T
C157737T
C161152T
C179537T

There's another branch of the B.1 polytomy that appears to satisfy the lineage designation criteria, defined by SNP 5595

This mutation is in the inverted terminal repeat - so there's a corresponding SNP at C191615T. This SNP does not appear in the Nextstrain tree because the 3' end is masked to prevent all ITR SNPs from appearing twice.

https://nextstrain.org/monkeypox/hmpxv1?c=gt-nuc_5595&m=div

Most of (sequenced) global B.1* circulation in 2023 falls into C.1, B.1.20 and the proposed lineage in #34

The second biggest lineage in 2023 that is still B.1 behind #34 is a lineage sequenced 13 time in Germany in late 2023.

In 2022, the lineage was also found once in Belgium, and the ancestor was also found in Australia and the US.

https://next.nextstrain.org/mpox/lineage-B.1?branchLabel=aa&gt=nuc.101418T

Defining mutations (broad):

• C34784T (unique, i.e. has not occurred elsewhere within B.1 yet)
• C101418T(unique, i.e. has not occurred elsewhere within B.1 yet)

There's a big US lineage that has also been seen once in Colombia with C18133T, G67611A, G130231A, G159277A

https://nextstrain.org/monkeypox/hmpxv1/2022-09-22?c=gt-nuc_67611,130231,159277&label=id:d0f9a0ce&m=div

There's a cluster of 4 sequences with recent circulation in the UK. It was previously identified in Nigeria.

To my knowledge this is the cluster that UKHSA called A.3 in a recent technical report. So it would make sense to give this also the official name A.3 here.

https://nextstrain.org/staging/monkeypox/hmpxv1/big?m=div

Defining mutations (reading off the branch mutations):

Unique (3) :G96841A, C100971T, C134078T
Homoplasies (3 ):G61844A, C84008T, C151050T

Sequences: OP536812, OP413718, MK783033, MG693723

Most of (sequenced) global B.1* circulation in 2023 falls into C.1 or B.1.20.

However, there's a third lineage that's currently part of B.1 that's been sizeable in the US alongside B.1.20 with sequences throughout 2023:

Defining mutations (broad):

• C132698T
• G22415A (unique, i.e. has not occurred elsewhere within B.1 yet)

All sequences just basal to the lineage are from Portugal. One sequence within the proposed lineage was sequenced in Portugal.

https://next.nextstrain.org/mpox/lineage-B.1?gt=nuc.22415A

There's a lineage that makes up the majority of sequences from Colombia - but is also present across Europe.

It's defined by: 89906T and G94798A on top of the B.1 polytomy

https://nextstrain.org/monkeypox/hmpxv1/2022-09-22?label=id:a12ef095&m=div

There's another candidate for a B.1 lineage designation with defining mutation C159779T (unique so far, good sign!) with detected circulation in 5 countries: Germany, France, Sweden, Portugal, US

https://nextstrain.org/staging/monkeypox/hmpxv1/big?c=gt-nuc_159779&m=div

it might be useful to auto-generate a markdown file with more or less the same content as the lineage.json, possibly with links to parent and the reference sequences (links can be generated like this https://www.ncbi.nlm.nih.gov/nuccore/MN023423).

This is the largest branch on the tree, not counting already labeled lineages.
https://nextstrain.org/groups/illinois-gagnon-private/monkeypox/0928

This mutation carries the amino acid change OPG204: D188N

Earliest sample with firm date: 6/17/2022
Latest sample with firm date: 8/04/2022 (The german sample has only 08/2022 as a collection date)

All but one of the samples have secondary mutation C132520T. There are another two samples with G175093A but without C132520T, but they've been sorted elsewhere on the tree. They are hMPX/Human/USA/CA-LAC-PHL-MA00092 and MA00096.

Description

Sublineage of: B.1.3
Earliest sequence: 2022/09 (Japan-Tokyo)
Most recent sequence: 2023/06/15 (China-Zhejiang)

This proposed sublineage of B.1.3 is defined by nuc mutation G109523A.

There are up to now 45 sequences, mainly from Japan-Tokyo (39 seqs), and also from Japan-Osaka (1 seq), Taiwan (4 seqs) and China-Zhejiang (1 seq).

It makes up for 42/48 sequences collected in Asia since January 1st 2023.

Genomes:

EPI_ISL_17959216, EPI_ISL_17445514, EPI_ISL_17959214, EPI_ISL_17959215, EPI_ISL_17445517, EPI_ISL_17809521, EPI_ISL_17445518, EPI_ISL_17445515, EPI_ISL_17445516, EPI_ISL_17445519, EPI_ISL_17428283, EPI_ISL_17592666, EPI_ISL_17592667, EPI_ISL_17592668, EPI_ISL_17817239, EPI_ISL_17837266, EPI_ISL_17592669, EPI_ISL_17837267, EPI_ISL_16905443, EPI_ISL_17837268, EPI_ISL_16905444, EPI_ISL_17592665, EPI_ISL_17152764, EPI_ISL_16905442, EPI_ISL_17152843, EPI_ISL_17428286, EPI_ISL_17762484, EPI_ISL_17762485, EPI_ISL_17008293, EPI_ISL_17665625, EPI_ISL_17722468, EPI_ISL_17008294, EPI_ISL_17665626, EPI_ISL_17008295, EPI_ISL_17665627, EPI_ISL_17008296, EPI_ISL_17518107, EPI_ISL_17665624, EPI_ISL_17246657, EPI_ISL_17246659, EPI_ISL_17692268, EPI_ISL_17817240, EPI_ISL_17592670, EPI_ISL_17817241, EPI_ISL_17692269

Hello everyone, I think this is the official site for hmpxv proposals, then I'm using the same pango-lineage format. This is the current observation.

Description

Potential new hmpxv B.1* lineage identified in Peru and defined by mutation G111029A and a nested sub-clade defined by G102694A. Observation was conducted by the Genomic Surveillance of the Instituto Nacional de Salud (INS) from Peru.

Genomes
Earliest sequence: 2022-06-25
Most recent sequence: 2022-07-24

Countries circulating
Major clade: Peru, 65
Minor clade (sub-clade) : Peru, 6
Major_clade.txt
Minor_clade.txt

Evidence
Major Clade

Minor Clade