Closed corneliusroemer closed 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
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
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 |
Thanks @corneliusroemer From what I can see, this recombinant still has only 9 or 10 genomes so will close this one for now
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:
Can be tracked via covSpectrum: https://cov-spectrum.org/explore/United%20States/AllSamples/Past6M/variants?aaMutations=S%3A346K&nucMutations=A13428G%2CG12793T
Full mutational signature: