[SHORT THREAD] On the now published paper purporting to show evidence that SARS-CoV-2 integrates into the human genome. I was unconvinced at the preprint, and I guess you will be unsurprised to hear that I remain skeptical. 1/n

Its not that this data is not suggestive of this possibility. The cell line data provide a nice proof of principle of integration, in an artificial system that lends itself to this sort of thing. 2/n

We have known its possible to induce viruses that don’t normally integrate to do so, for LCMV for example, for a while. It is also the case that LINE mediated integration of non-retroviral viruses has previously been shown for other single stranded viruses, like bornaviruses 3/n

Indeed my team has shown that all 7 ‘Baltimore group’ genome types, can very occasionally integrate. The trouble is, coronaviruses, despite an extensive search for integrations, have never been shown to do so, so this is a strong claim and therefore requires strong evidence 4/n

Ultimately, the killer experiment - an integrated host/virus integration site from a naturally infected patient, is still missing in this manuscript. I appreciate this is a very hard experiment to do, and therefore relying on next gen approaches may be the best we can do. 5/n

However, there are known artefacts that can cause the kind of chimeric reads seen here, and these still cannot be ruled out, and the hypothesis of an integrated coronavirus remains just that; a hypothesis. 6/n