Reverse-transcribed SARS-CoV-2 RNA can integrate into the genome of cultured human cells '...' expressed in patient-derived tissues, 2021, Zhang et al

Abstract
Prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA and recurrence of PCR-positive tests have been widely reported in patients after recovery from COVID-19, but some of these patients do not appear to shed infectious virus. We investigated the possibility that SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the DNA of human cells in culture and that transcription of the integrated sequences might account for some of the positive PCR tests seen in patients. In support of this hypothesis, we found that DNA copies of SARS-CoV-2 sequences can be integrated into the genome of infected human cells. We found target site duplications flanking the viral sequences and consensus LINE1 endonuclease recognition sequences at the integration sites, consistent with a LINE1 retrotransposon-mediated, target-primed reverse transcription and retroposition mechanism. We also found, in some patient-derived tissues, evidence suggesting that a large fraction of the viral sequences is transcribed from integrated DNA copies of viral sequences, generating viral–host chimeric transcripts. The integration and transcription of viral sequences may thus contribute to the detection of viral RNA by PCR in patients after infection and clinical recovery. Because we have detected only subgenomic sequences derived mainly from the 3′ end of the viral genome integrated into the DNA of the host cell, infectious virus cannot be produced from the integrated subgenomic SARS-CoV-2 sequences.
Continuous or recurrent positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PCR tests have been reported in samples taken from patients weeks or months after recovery from an initial infection (1⇓⇓⇓⇓⇓⇓⇓⇓⇓⇓⇓⇓⇓⇓⇓–17). Although bona fide reinfection with SARS-CoV-2 after recovery has recently been reported (18), cohort-based studies with subjects held in strict quarantine after they recovered from COVID-19 suggested that at least some “re-positive” cases were not caused by reinfection (19, 20). Furthermore, no replication-competent virus was isolated or spread from these PCR-positive patients (1⇓–3, 5, 6, 12, 16), and the cause for the prolonged and recurrent production of viral RNA remains unknown. SARS-CoV-2 is a positive-stranded RNA virus. Like other beta-coronaviruses (SARS-CoV-1 and Middle East respiratory syndrome-related coronavirus), SARS-CoV-2 employs an RNA-dependent RNA polymerase to replicate its genomic RNA and transcribe subgenomic RNAs (21⇓⇓–24). One possible explanation for the continued detection of SARS-CoV-2 viral RNA in the absence of virus reproduction is that, in some cases, DNA copies of viral subgenomic RNAs may integrate into the DNA of the host cell by a reverse transcription mechanism. Transcription of the integrated DNA copies could be responsible for positive PCR tests long after the initial infection was cleared. Indeed, nonretroviral RNA virus sequences have been detected in the genomes of many vertebrate species (25, 26), with several integrations exhibiting signals consistent with the integration of DNA copies of viral mRNAs into the germline via ancient long interspersed nuclear element (LINE) retrotransposons (reviewed in ref. 27). Furthermore, nonretroviral RNA viruses such as vesicular stomatitis virus or lymphocytic choriomeningitis virus (LCMV) can be reverse transcribed into DNA copies by an endogenous reverse transcriptase (RT), and DNA copies of the viral sequences have been shown to integrate into the DNA of host cells (28⇓–30). In addition, cellular RNAs, for example the human APP transcripts, have been shown to be reverse-transcribed by endogenous RT in neurons with the resultant APP fragments integrated into the genome and expressed (31). Human LINE1 elements (∼17% of the human genome), a type of autonomous retrotransposons, which are able to retro-transpose themselves and other nonautonomous elements such as Alu, are a source of cellular endogenous RT (32⇓–34). Endogenous LINE1 elements have been shown to be expressed in aged human tissues (35) and LINE1-mediated somatic retrotransposition is common in cancer patients (36, 37). Moreover, expression of endogenous LINE1 and other retrotransposons in host cells is commonly up-regulated upon viral infection, including SARS-CoV-2 infection (38⇓–40).

In this study, we show that SARS-CoV-2 sequences can integrate into the host cell genome by a LINE1-mediated retroposition mechanism. We provide evidence that the integrated viral sequences can be transcribed and that, in some patient samples, the majority of viral transcripts appear to be derived from integrated viral sequences.

https://www.pnas.org/content/118/21/e2105968118/tab-article-info

 

I am not sure if it fits here and I can't judge the quality of the study and the speculation regarding long covid and maybe ME/CFS. I hope it was not posted already.

I am regularly listening to a podcast with the German epidemiologist and virologist Alexander Kekule, who is my guide through the pandemic so far.

I was surprised when he mentioned ME/CFS during one episode while discussing long covid. He said that many of the symptoms of long covid are well known from ME/CFS which is often triggered by other viral infections and which is well known by neurologists. I was very surprised that he mentioned ME/CFS, that he actually called it ME, and more so that he presented it as an established diagnosis especially within neurology (I never came across a neurologist who was aware of ME/CFS).

Lately he presented the study above. And as a side note he said something regarding long covid and this study.

I am paraphrasing here. He said, that if the results of this study were correct, one could speculate if the integration of virus sequences into the DNA of the host can result in (some of) the neurological symptoms seen in long covid (and therefore maybe ME/CFS?).

As I understood it, the study results, if correct, show for the first time (?) the reverse transcripton of RNA into DNA, and the integration of the virus sequences into host DNA, of a non retro virus. Long interspersed nuclear elements (Line1) would be able to reverse viral RNA into DNA and build the virus sequences into the DNA of the host, where the integrated sequences are not able to produce infectious virus like retro viruses do, but produce proteins to which the immune system could potentially react.
Line 1 seems to be upregulated in neurological diseases and in viral infections, especially in nerve cells.

So I understand the reasoning for his speculation to be:

upregulated Line 1 in nerve cells reverses Virus RNA into DNA that is built into host DNA and produces proteins to which the immune system reacts and that could lead to ongoing neurological symptoms,even if there ist no active viral infection.

I hope I got this right.

Long Covid really was not the reason why he discussed this and him speculating about long covid in this context sure was not the result of days of thinking it through, but if I understood everything correctly, could the study results,if true, actually have implications for Long Covid and ME/CFS and is this valid reasoning or is this nonsense or something that is off the table already?

This explanation probably would leave out the PWME who had no obvious viral trigger.
Also the study refers to SARS Cov 2 and not other viruses.
And if PCR tests would be positive due to transcripton of the integrated viral DNA, as mentioned in the study, wouldn't ME/CFS studies which looked for viral infections already have detected a link between ME/CFS and positive PCR tests?

 

Struggling with reading comprehension this evening so may completely have got the wrong end of the stick, but are we looking at two possibilities for long term conditions

1. The incorporation of virus RNA into the individual human’s DNA which is then replicated by normal cell devision. Presumably once the active virus infection is over, this replicated virus RNA can not spread in most instances beyond the specific locations it was originally incorporated, as say liver cells do not say normally migrate beyond the liver. This would suggest that any impact on the normal functioning of biological systems due to genetically altered tissue would remain localised, though obviously the original active viral infection could have colonised the DNA in multiple locations. (However, if cells containing the altered DNA did migrate presumably they could not ‘infect’ other tissues, though they could theoretically crop up else where as tumours.)
2. The presence of virus RNA incorporated into the human DNA when reproduced in normal cell devision is picked up as ‘alien’ and results in an immune response attacking the bodies own tissues, which is the cause of ongoing symptoms.

This would presumably imply the severity of any ongoing infection should be proportional to the viral load of the initial infection, which does not appear to necessarily be the case with either Long Covid or with ME, unless you proposed an additional factor where the person’s susceptibility to virus RNA colonisation of their own DNA varies between individuals.

 

Here is an easy to understand article:

https://www.sciencemag.org/news/202...-pandemic-coronavirus-can-integrate-human-dna

However a new article came out about a group that found that it's unlikely the PNAS results are correct:

https://www.purdue.edu/newsroom/rel...-material-into-human-dna,-research-shows.html

Hard to say who will be right in the end.