You raise an important question. Most Sequencing is being done with ARTIC primer pairs and such recombination events may be missed. The place to look is in random priming methods used in RNA-Seq data. There is now a lot of this data in the SRA. I have not had time to sleuth through it as Im still trying to find the Bivalent vaccine sequences. If anyone can find these, it would be a huge help. I checked the NEJM paper, the Clinical Trial docs in clinicaltrials.gov, the paper supplement, some FDA documents... Cant find them.