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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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MV.1 + ORF1b:K2557R (40) + ORF1a:S2103F (26, Singapore) #2149

Open Fearuncle opened 1 week ago

Fearuncle commented 1 week ago

image tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_60f5_b40c10.json?f_userOrOld=uploaded%20sample

First Seq: 2024-07-20 Most Recent: 2024-10-02

Gisaid: A21137G, C936T, C21627A (edited) Gisaid for Orf1a:S2103F sub branch: A21137G, C936T, C6573T (mainly Singapore) (edited)

PQ432138.1 EPI_ISL_19467870 EPI_ISL_19437940 EPI_ISL_19467950 EPI_ISL_19420685 EPI_ISL_19336983 EPI_ISL_19390513 EPI_ISL_19467948 EPI_ISL_19420677 EPI_ISL_19467818 EPI_ISL_19373003 EPI_ISL_19467842 EPI_ISL_19467802 EPI_ISL_19467919 EPI_ISL_19467873 EPI_ISL_19467911 EPI_ISL_19467844 EPI_ISL_19464449 EPI_ISL_19467850 EPI_ISL_19437370 EPI_ISL_19467822 EPI_ISL_19467892 EPI_ISL_19467914 EPI_ISL_19467878

FedeGueli commented 6 days ago

ORF1a:S2103F is close to 50K samples sparse in most of the fast lineages of the Pandemic. likely not deleterious. In fact Bloom and Neher scored it as beneficial

Screenshot 2024-10-13 alle 12 36 42

@alurqu could you check for recent variants please?

FedeGueli commented 6 days ago

@Fearuncle i have adjusted the queries separating the main and the sub lineage

FedeGueli commented 6 days ago

the ORF1a:S2103F is Singapore only , likely a cluster. Hence its growth advantage (ahead of everything) should be taken with a grain of salt.

alurqu commented 6 days ago

@alurqu could you check for recent variants please?

Bloom and Neher fitness estimates for ORF1aLS2103F across all clades for which estimates are available:

clade,gene,aa_mutation,delta_fitness 20A,ORF1ab,S2103F,1.0088 20B,ORF1ab,S2103F,1.0866 20C,ORF1ab,S2103F,1.3487 20E,ORF1ab,S2103F,1.1428 20G,ORF1ab,S2103F,1.2279 20H,ORF1ab,S2103F,1.4357 20I,ORF1ab,S2103F,1.3698 20J,ORF1ab,S2103F,1.3659 21C,ORF1ab,S2103F,1.2679 21I,ORF1ab,S2103F,1.0466 21J,ORF1ab,S2103F,1.0928 21K,ORF1ab,S2103F,0.76662 21L,ORF1ab,S2103F,1.2247 22A,ORF1ab,S2103F,1.2061 22B,ORF1ab,S2103F,1.0717 22C,ORF1ab,S2103F,1.1527 22D,ORF1ab,S2103F,1.0019 22E,ORF1ab,S2103F,0.82584 22F,ORF1ab,S2103F,1.0542 23A,ORF1ab,S2103F,1.0988 23B,ORF1ab,S2103F,1.1919 23C,ORF1ab,S2103F,0.95542 23D,ORF1ab,S2103F,0.60712 23E,ORF1ab,S2103F,0.99946 23F,ORF1ab,S2103F,0.92266 23H,ORF1ab,S2103F,0.24313 23I,ORF1ab,S2103F,1.037

So ORF1a:S2103F likely increases viral fitness a little but not a lot.

Unfortunately there are not yet any estimates available for mutation relative fitness on clades designated after 23I (BA.2.86).

FedeGueli commented 6 days ago

@alurqu could you check for recent variants please?

Bloom and Neher fitness estimates for ORF1aLS2103F across all clades for which estimates are available:

clade,gene,aa_mutation,delta_fitness 20A,ORF1ab,S2103F,1.0088 20B,ORF1ab,S2103F,1.0866 20C,ORF1ab,S2103F,1.3487 20E,ORF1ab,S2103F,1.1428 20G,ORF1ab,S2103F,1.2279 20H,ORF1ab,S2103F,1.4357 20I,ORF1ab,S2103F,1.3698 20J,ORF1ab,S2103F,1.3659 21C,ORF1ab,S2103F,1.2679 21I,ORF1ab,S2103F,1.0466 21J,ORF1ab,S2103F,1.0928 21K,ORF1ab,S2103F,0.76662 21L,ORF1ab,S2103F,1.2247 22A,ORF1ab,S2103F,1.2061 22B,ORF1ab,S2103F,1.0717 22C,ORF1ab,S2103F,1.1527 22D,ORF1ab,S2103F,1.0019 22E,ORF1ab,S2103F,0.82584 22F,ORF1ab,S2103F,1.0542 23A,ORF1ab,S2103F,1.0988 23B,ORF1ab,S2103F,1.1919 23C,ORF1ab,S2103F,0.95542 23D,ORF1ab,S2103F,0.60712 23E,ORF1ab,S2103F,0.99946 23F,ORF1ab,S2103F,0.92266 23H,ORF1ab,S2103F,0.24313 23I,ORF1ab,S2103F,1.037

So ORF1a:S2103F likely increases viral fitness a little but not a lot.

Unfortunately there are not yet any estimates available for mutation relative fitness on clades designated after 23I (BA.2.86).

thank you!

FedeGueli commented 5 days ago

+12 Singapore

DailyCovidCases commented 23 minutes ago

@FedeGueli Propose this branch?