The data presented in this preprint are unconvincing and insufficient to claim SARS-CoV-2 is reverse-transcribed and integrated in the human genome. Many have already pointed out the flaws, but here is a summary. 1/n https://twitter.com/biorxiv_genomic/status/1338235108936052738

To prove L1-mediated retrotransposition events, the standard in the field is to show sequence of integrants along with flanking genomic sequences. Here they show exactly zero.

If L1 is involved one expect to see: target site duplication (short direct repeats flanking integrant), integration at preferred EN cleavage site (TTTT/AA), polyA tail at the 3’ end (or chimerism with L1/Alu 3' end). Authors report none of these hallmarks.

Again that's b/c they do not isolate/sequence any integration events, neither from infected patient or cell culture experiments. qPCR and RNA-FISH are inadequate to prove genomic integration.

There are unaddressed pitfalls with the analysis of chimeric reads in Fig 1: artifacts of RNA-seq library prep or real template-switching events from Cov-2 subgenomic RNA to cellular mRNAs (which would be unsurprising). More on this issue here: https://twitter.com/mw_fr/status/1338275889268760576?s=20

Regardless of these pitfalls, chimeric RNA-seq reads CANNOT be taken as evidence for viral integration in the human genome!

Experiments in cell culture (Fig 2) with L1 overexpression are artificial and no more convincing: no integrant are isolated/sequenced and they lack important controls such as RT mutant.

Even if, cell culture assays would only show retrotransposition of SARS-Cov-2 RNA is possible in principle (unsurprisingly since one can make any RNA retrotranspose in cell culture), but not that it happens in people.

IMO it is dangerous given the current climate to have a preprint out with that title unsubstantiated, coming from such prominent scientists. I am concerned and urge the authors to withdraw their preprint. /fin