The paper may be reliable in its finding that
"BNT162b2 mRNA is reverse transcribed intracellularly into DNA in as fast as 6 h upon BNT162b2 exposure",
however, the authors apparently refrained from trying to find integration into the genome of the hepatitic cells. They do not claim to have found integration into the genome. They say,
"(f)urther studies are needed to demonstrate the effect of BNT162b2 on genomic integrity, including whole genome sequencing of cells exposed to BNT162b2, as well as tissues from human subjects who received BNT162b2 vaccination."
In that context they do not refer to a previous study which - before the question had been edited anew - had been linked to: Zhang et al., Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells and can be expressed in patient-derived tissues. Interestingly, this study did not use tissues from human subjects who received vaccine (or had been infected), however in their setup used whole genome sequencing to detect recombinded virus-host-DNA. This study did not.
Isn't whole genome sequencing easy to do these days? Was there a lack of "tissues from human subjects"? In fact, mentioned previous study by Zhang et al. (on virally infected cells) recurred to existing RNA-analysis (existing data) when trying to find out about normal cells, after they had examined artificially LINE1-upregulated cells in vitro. That may hint to what does not go without saying, which neither the study challenged by question nor its co-study mentioned above explains and elaborates on, and only to experts seems obvious and apparent:
The study questioned did not undertake to prove whether retrotranscribed DNA - which was undebatedly found - is of host cell genome origin (post integration) or of viral origin (post retro-transcription).
Both studies do not speak of "free viral cellular DNA". That may be some blunt way to describe the issue, however, first, the technique of recombinant DNA vaccine shows very cleary (and very unexpectedly) that DNA in cells may exist without being integrated into the genome of the host cell. Adenovirus vector technique is based on viral DNA in cells not being integrated into the genome (There is no finding of vaccine recombinant DNA being retro-transcibed into the genome (after transcription to m-RNA)).
Second, it is accepted knowledge that several virus species persist latently in host cells in so called episomal form. E.g. herpes virus DNA is known to persist episomally in the nucleus without integrating into the host cell's genome. The following quote refers to adeno associated virus (different from Adenovirus used in vaccine): "Although AAV vector genomes can persist within cells as episomes, vector integration has been observed in various experimental settings, either at non-homologous sites where DNA damage may have occurred or by homologous recombination." Deyle and Russell, Adeno-associated virus vector integration; see also, e.g., Chong et al.Transfection types (...): "Stable transfection refers to (...) integrating foreign DNA into the host nuclear genome or maintaining an episomal vector in the host nucleus as an extra-chromosomal element (...). The transgene may then be constitutively expressed even with the replication of cells (...). In contrast, transient transfection does not require integrating nucleic acids into the host cell genome (...)"
This shows that retrotranscription as a first step may very well be distinguished and proved independently from integration into the genome.
The study in question here proved retro-transcription of vaccine m-RNA. Different from Zhang et al. they did not do any "whole genome sequencing" to find out about integration. The authors do not give reasons. In case of positive findings, we still wouldn't know if CoV-DNA integrates in normal tissue.
Whereas the first study searched for
i.e. DNA sequences that comprise quote "partial (...) subgenomic RNA sequence that was flanked by a duplicated host cell DNA target sequence" to lay proof of integration into the genome, the study challenged here did not. You will not find the word "chimeric transcript" being mentioned in the description of the methods employed:
"Genomic DNA was extracted from cell pellets ... PCR was then performed using primers targeting BNT162b2 (sequences are shown in Table 1) (Remark:no chimeric sequences among) ... Bands corresponding to the amplicons of the expected size (444 bps) were cut out and DNA was extracted ... The sequence of the DNA amplicon was verified by Sanger sequencing."
However, it seems unanimously accepted that chimeric transcripts are valid proof of integration - if validly found. The latter had been questioned by peer review in respect of the study by Zhang et al.
To sum up: There is no reason given for not using "long sequencing" technique that might have found chimeric transcripts. Alternatively, the study might have given reasons why chimeric transcripts cannot be accepted as proof of integration. The study questioned here seems to self-restrict itself in significance and reach.
It may be some biased opinion to think of the previous study having been reviewed as technically not valid in respect of its findings of chimeric transcripts as a reason why the study challenged here refrained from long sequence technique (Remark: mentioned previous study did not either in respect of tissue from patients, in its non in vitro follow up, as it then used pre-existing data that resulted from RNA, not DNA search and sequencing which in my opinion might explain the artifacts they were blamed for).
Final remarks: Merits of this study may lie in the use of nano lipids in combination with cancer cells. It had been shown before that any cell can possibly uptake the nanolipids; however, in respect of the previous study by Zhang et al., this study results in some strong argument for LINE1-expression not being dependent either on artifically induced over-expression nor - as it used nano lipids - on viral infection (host-virus membrane fusion or receptor mediated endocytosis). Natural infection may very well appear as a prerequisite for upregulation of LINE1.
Still, any study might be challenged for not being "reliable" or "serious" (quote pre-edited version of this question), in my opinion, as long as the mechanism of LINE1 activation, of inducing LINE1, remains unknown.
There are no known side-effects of LINE1 integrating DNA, and they have not been searched on by the study questioned nor are there any other studies up to date on effects of CoV-DNA integration. It is beyond the scope of this study to offer cues that hint at chimeric transcripts (integration) coresponding (not to side-effects but) to severity of disease (Zhang et al.: "...in some patients-derived tissues ... a large fraction of the viral transcripts could have been transcribed from SARS-CoV-2 sequences integrated into the host genome.")