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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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Proposal for a potential delta lineage with ORF3a:D238Y (~6.5K sequences), and its sub-lineage with S:S680T (802 sequences) #267

Closed c19850727 closed 2 years ago

c19850727 commented 3 years ago

Description: Sub-lineage of: B.1.617.2, Clade 21J (~6.5K sequences) Earliest sequence: 2021/2/1 (India) Most recent sequence: 2021/10/12 (Denmark) Countries circulating: fairly wide-spread worldwide, with highest prevalence in Mozambique

Mutations in addition to B.1.617.2: ORF1a:K261N, then ORF3a:D238Y

Genomes: Delta D238Y.csv

Evidence:

Number of samples sequenced as per outbreak.info: image https://outbreak.info/situation-reports?pango&muts=ORF3a%3AD238Y&muts=ORF1a%3AK261N

Downsized tree as per NeherLab: image https://nextstrain.org/groups/neherlab/ncov/africa-mozambique?c=gt-ORF3a_238&f_clade_membership=21J%20%28Delta%29&label=spike_mutations:I95T&p=grid&r=division

Transmission advantage as per CoV-Spectrum: image https://cov-spectrum.ethz.ch/explore/World/AllSamples/AllTimes/variants/json=%7B%22variant%22%3A%7B%22mutations%22%3A[%22ORF3a%3AD238Y%22%2C%22ORF1a%3A261N%22]%7D%2C%22matchPercentage%22%3A1%7D

image

Noticeably there's a branch with additional S:S680T within this clade, which is geographically more concentrated, and grows considerably faster.

Description: Sub-lineage of: B.1.617.2, Clade 21J (802 sequences) Earliest sequence: 2021/6/17 (Armenia) Most recent sequence: 2021/10/12 (Denmark) Countries circulating: some European countries

Cumulative prevalence and number of samples sequenced as per Outbreak.info: image

Mutations in addition to B.1.617.2: ORF1a:K261N, then ORF3a:D238Y then C4455T and ORF1a:A1397V and ORF1b:A1643V and S:S680T

Genomes: Delta D238Y+S680T.csv

Evidence UsHER subtree: image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_d424_e63470.json?c=gt-S_680&l=radial

Downsized tree as per NeherLab: image https://nextstrain.org/groups/neherlab/ncov/sweden?c=gt-S_680&f_clade_membership=21J%20%28Delta%29&label=spike_mutations:I95T&p=grid&r=division

Transmission advantage as per CoV-Spectrum: image https://cov-spectrum.ethz.ch/explore/World/AllSamples/AllTimes/variants/json=%7B%22variant%22%3A%7B%22mutations%22%3A[%22ORF3a%3AD238Y%22%2C%22ORF1a%3A261N%22%2C%22S%3AS680T%22]%7D%2C%22matchPercentage%22%3A1%7D

shay671 commented 3 years ago

the 680 mutation subvariant seems to have a mutational jump : 6 mutation jump 4/6 Non synonymous 2 mutations in converged sited (Furin cleavage site & orf3a).

Above that.- there is a subvariant for that subvariant with RBM mutation (position 427) with 148 seq

corneliusroemer commented 3 years ago

This issue needs to be considered together with my comment here: https://github.com/cov-lineages/pango-designation/issues/268#issuecomment-946881724 since the two issues derive from the same branch with ORF1a:261N

FedeGueli commented 2 years ago

The parental lineage has now been designated as AY.122 in #320 .

maybe it would be useful to close this and repropose?

@corneliusroemer

chrisruis commented 2 years ago

It doesn't look like these clades have expanded relative to the rest of AY.122 so I'll close this for now