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Potential US East Coast BA.1.1/AY.119* recombinant (7 seq) [potentially the one monitored by UKHSA] #439

Closed corneliusroemer closed 2 years ago

corneliusroemer commented 2 years ago

I saw that UKHSA is monitoring a potential AY.119.2/BA.1.1 recombinant. I couldn't find an issue so I tried to figure out which cluster they meant.

This was one here was noticed amongst others by @c19850727, potentially someone else before.

EPI_ISL_8720194, 8981459, 8981712, 8981824, 9088187, 9147438, 9147935

Locations: US-MA, PA, NJ, TN

First sequence: 2021-12-31

Breakpoint: between Spike NTD/RBD nuc 22199-22576

Key mutations:

ORF1a:A2855V (AY.119*)
ORF1a:K4176N (AY.119.2)
ORF1b:A1847S (AY.119*)
S:R346K (BA.1.1)
ORF7b:S5P (BA.1*)

Can be tracked via covSpectrum: https://cov-spectrum.org/explore/United%20States/AllSamples/Past6M/variants?aaMutations=S%3A346K&nucMutations=A13428G%2CG12793T

image

Full mutational signature:

image
1GHX commented 2 years ago

So how many recombinant clusters are there in the UK? I've also seen this UK recombinant cluster, shared by Tom Peacock: EPI_ISL_8610834, 8865709, 8898412, 9026013, 9062592, 9125312, 9175215, 9296739

Source: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_28218_979b40.json?branchLabel=Spike%20mutations&c=pango_lineage_usher&label=nuc%20mutations:A11201G,A11332G,G11537A,C13195T,T15240C,G15451A,C23664T

corneliusroemer commented 2 years ago

Wrong thread @1GHX, this issue is about a US cluster, see #441 and #422 for the 2 UKHSA monitored UK clusters.

Here are the sequences from NCBI: https://pastebin.com/raw/zqVmTDae

And in Nextclade: https://clades.nextstrain.org/?dataset-name=sars-cov-2&input-fasta=https://api.allorigins.win/raw?url=https://pastebin.com/raw/zqVmTDae

Here split at the breakpoint: https://clades.nextstrain.org/?dataset-name=sars-cov-2&input-fasta=https://api.allorigins.win/raw?url=https://pastebin.com/raw/rsesjgMp

kristinelacek commented 2 years ago

CDC has confirmed 9 samples belonging to this potential lineage, resulting from recombination between AY.119.2 and BA.1.1 Preprint here.

Pangolin currently assigns lineage of "None"

Collection Date State GISAID Accession GISAID Virus Name NCBI Accession NCBI Name BioSample Accession
12/31/2021 Tennessee EPI_ISL_8720194 hCoV-19/USA/TN-CDC-ASC210559252/2021 OM272834 SARS-CoV-2/Human/USA/TN-CDC-ASC210559252/2021 SAMN24974483
1/4/2022 Pennsylvania EPI_ISL_8981459 hCoV-19/USA/PA-CDC-LC0474301/2022 OM344043 SARS-CoV-2/Human/USA/PA-CDC-LC0474301/2022 SAMN25170048
1/4/2022 Pennsylvania EPI_ISL_8981712 hCoV-19/USA/PA-CDC-LC0473996/2022 OM344166 SARS-CoV-2/Human/USA/PA-CDC-LC0473996/2022 SAMN25170131
1/4/2022 Pennsylvania EPI_ISL_8981824 hCoV-19/USA/PA-CDC-LC0474055/2022 OM344238 SARS-CoV-2/Human/USA/PA-CDC-LC0474055/2022 SAMN25170117
1/4/2022 New Jersey EPI_ISL_9147438 hCoV-19/USA/NJ-CDC-IBX952397337138/2022 OM392955 SARS-CoV-2/Human/USA/NJ-CDC-IBX952397337138/2022 SAMN25262195
1/12/2022 Massachusetts EPI_ISL_9088187 hCoV-19/USA/MA-CDC-STM-HZEBR92XC/2022 OM372355 SARS-CoV-2/Human/USA/MA-CDC-STM-HZEBR92XC/2022 SAMN25233756
1/12/2022 New Jersey EPI_ISL_9147935 hCoV-19/USA/NJ-CDC-IBX640654818289/2022 OM393452 SARS-CoV-2/Human/USA/NJ-CDC-IBX640654818289/2022 SAMN25262455
2/12/2022 New Jersey EPI_ISL_10389336 hCoV-19/USA/NJ-CDC-ASC210553977/2022 OM835119 SARS-CoV-2/Human/USA/NJ-CDC-ASC210553977/2022 SAMN26256159
2/12/2022 New Jersey EPI_ISL_10389339 hCoV-19/USA/NJ-CDC-ASC210553978/2022 OM835120 SARS-CoV-2/Human/USA/NJ-CDC-ASC210553978/2022 SAMN26256158
chrisruis commented 2 years ago

Thanks @corneliusroemer From what I can see, this recombinant still has only 9 or 10 genomes so will close this one for now