Novel recombinants

[szhan]

We want a list of novel recombinants satisfying the following criteria:

• At least 1 descendant sample (see Recombination landscape #303)
• Max run length of at most 2 (see False positive recombinants associated with deletions (e.g. under Delta) #279)
• Not Pango X
• Not Jackson et al. (see Jackson et al. recombinants #293)
• Not Delta or Omicron "origin" (see Is Delta (B.1.167.2) a recombinant? #258 and Recombinant backbone #297)

Then, we want to run 3SEQ on them.

Also, we'd like to get Kat's eyes on the good/interesting ones.

[szhan]

Some notes. In v1-beta1_2023-02-21.dated.il.tsz.

recombinant	descendants	sample	sample_pango	comment
200039	538258	200038	B.1.617.2	Delta origin
822854	284834	822853	BA.2	BA.2 origin
1189192	112781	1189178	BA.5.1	BA.5 origin
1030562	112298	1030561	BA.2	artifact h/t Yan

Also, these two one-sample recombinant nodes are labelled XAS: 1269074 and 1278385.

[szhan]

Applying the above filtering criteria, I'm getting 173 novel recombinants to further examine.

[szhan]

@ktmeaton Please feel free to comment and/or discuss your analysis here!

[ktmeaton]

Before diving in too deep, I just want to confirm that I'm working with the correct source files:

• sc2ts Novel Recombinants: https://github.com/jeromekelleher/sc2ts-paper/blob/main/data/recombinants.csv
• Viridian Metadata: https://doi.org/10.6084/m9.figshare.27195261
• Viridian Consensus Sequences: https://doi.org/10.6084/m9.figshare.25713225

[szhan]

That link goes to the metadata v05 file, which combines info for the batch 1 and batch 2 sequences. We are only using the batch 1 sequences in the metadata v04 file, which can be found here: https://figshare.com/articles/dataset/Supplementary_table_S1/25712982?file=45969195