What does HackerNews think of PRJNA692319_public?
Analysis of Antarctica sequencing samples contaminated with SARS-CoV-2
It's easy to say this, as neither you nor I have the requisite knowledge to prove/disprove your assertion. But I read threads like this one [1] or resources like this one [2] and realize that there are experts who are able to distinguish earlier and later variants.
Incidentally, I noticed that you edited your first response several times while I wrote this. The tone of what you wrote first was a bit less considered than the what I'm responding to now, but I hope it's ok to just leave it at this.
After doing some in-depth research to find the original research or reports I've found nothing published by the Hungarian institutions nor Dr Jesse Bloom - the only person quoted in the article. Having dug further I don't take his statements at face value either, for the reasons described below, since there's more than a hint of preconceived bias in his general thrust and previous publications.
I REALLY wish journalists would clearly share published sources to original research and data for such important events rather than stir up controversy without demonstrating a strong foundation. Especially when claiming this is a "finding".
For clarity, I've no opinion on SARS-Cov-2 origin but I do want to see claims well-supported by evidence.
I went looking on both the mentioned Hungarian web-sites [0][1], searched biorxiv, and checked the Bloom Lab [2] publications since the only person quoted is Jesse Bloom [3] who claims to have reproduced (Hungarian) results. In my research I also found a prior report by Bloom in June 2021 [4] reporting 'recovery of deleted files containing partial sequences' [4] that were soon criticised by multiple other scientists; e.g: "...The language of the paper is unusual, its contains a significant degree of supposition and conjecture, cites blog posts..." [5].
[0] https://univet.hu/en/research/topics/
[1] https://www.elte.hu/en/facts
[2] https://research.fredhutch.org/bloom/en/publications.html
[3] https://research.fredhutch.org/bloom/en/members.html
[4] https://www.biorxiv.org/content/10.1101/2021.06.18.449051v1....
[5] https://edition.cnn.com/2021/06/23/health/coronavirus-sequen...
Updated: just discovered there's a recent github repo [6] created by Bloom with much more detail. Telegraph should really have pointed to this.
[6] https://github.com/jbloom/PRJNA692319_public
Update 2: Pre-print [7] of the Hungarian report (see [6] for details as to why it was rejected by Biorxiv several times).
particularly the end of README.md:
"On Feb-8-2022, I e-mailed the Chinese authors of the paper to ask about the sample deletion and restoration. They e-mailed back almost immediately. They confirmed what they had told Istvan: they had sequenced the samples with Sangon Biotech (Shanghai) after extracting the DNA in December 2019 from their samples. The suspect that contamination of the samples happened at Sangon Biotech. They deleted the three most contaminated samples from the Sequence Read Archive. They do not know why the samples were then 'un-deleted.'"
(end quote)