Can COVID-19 Genes Integrate Into Human DNA?

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Respected experts in genetics have caused a stir on both social media and in scientific circles by suggesting that SARS-CoV-2 can integrate pieces of its genetic code into the human genome.

If true, the results could explain why some people test positive for SARS-CoV-2 RNA sometimes months after recovering from their initial infection, even though no infectious virus can usually be grown.

But many scientists say they aren’t convinced, citing concerns that the findings could simply be artifacts of lab preparation.

Some have also raised concerns that the work could be misconstrued by the anti-vaccine community, which is reportedly stretching the results to apply to COVID-19 vaccines — even though the authors have stressed the work has no implications for the vaccines. They also emphasized that there are no implications for human health at this time.

Initial Controversy

The controversy began in December 2020, when Rudolf Jaenisch, MD, a founding member of the Whitehead Institute for Biomedical Research at MIT, and colleagues published a preprint on bioRxiv suggesting that SARS-CoV-2 RNA could be reverse transcribed and integrated into the human genome.

The results, which weren’t peer-reviewed, set off a storm on #ScienceTwitter. They were panned on an episode of This Week in Virology (TWiV), and garnered harsh criticism from commenters who said they could be used to bolster false claims about vaccines.

“If there ever was a preprint that should be deleted, it is this one!” Marie-Louise Hammarskjöld, MD, PhD, a professor of microbiology at the University of Virginia, commented on the bioRxiv article. “It was irresponsible to even put it up as a preprint, considering the complete lack of relevant evidence. This is now being used by some to spread doubts about the new vaccines.”

Since then, at least two more preprints on the issue have been published on bioRxiv, in which researchers say they attempted to replicate the results but could not. The crux of their argument is that the results relied on published libraries of RNA sequencing data from SARS-CoV-2 infected cell cultures and organoids of the lung, heart, brain, and stomach, as well as COVID-19 patient-derived cells. Preparation of these RNA-sequencing libraries is error-prone and can also create chimeras. So the SARS-CoV-2 human chimeric transcripts could be lab artifacts created during the preparation of these libraries, not from natural infection, they argue.

Jaenisch acknowledged to MedPage Today that “there were holes in the argument,” that the evidence “was not complete,” and that “there was reason for criticizing this paper.”

He added that the unnamed journal where he was seeking publication required coronavirus papers to be posted on the bioRxiv server upon submission.

“In hindsight, it was a mistake,” he said. “I regret to have published this preprint. I didn’t want to do it, but I was sort of forced. We were under enormous pressure to make it known.”

Addressing Criticism Stirs More Controversy

Jaenisch and team subsequently performed additional analyses, which they published last month in PNAS, prompting another Twitter storm.

“Joining of #SARSCoV2 genome to cellular DNA is an artifact. The #PNAS paper describing this ‘finding’ should never have been published as it is biologically irrelevant,” tweeted Vincent Racaniello, PhD, of Columbia University, and host of the TWiV podcast.

Still, Jaenisch contends that the newest paper provides evidence that confirms “totally without doubt” two key results: small fragments of SARS-CoV-2 can integrate into the human genome, and these integrated viral sequences can be detected by PCR.

“Now, I think we have proven it. No one can doubt this, based on seeing DNA copies of the virus in the genome of infected cells. And, these sequences in patients have to come from integrated sequences, based on the structure that you would expect,” he told MedPage Today.

Although they acknowledge that they cannot rule out artifacts, Jaenisch and colleagues addressed the issue by looking at the orientation of integrated viral sequences compared to human genes. Reasoning that viral sequences should insert randomly, about 50% of them would be expected to be in the opposite (or negative-sense) direction. In their study, they found that around 40% of human-viral chimeric transcripts had negative-sense integrations in at least one patient-derived sample, although that percentage varied and was lower in other samples (mostly lung).

They also found that the integrated viral sequences were flanked by genetic elements characteristic of long interspersed nuclear elements-1 (LINE-1). About 17% of the human genome encodes these LINE-1 elements, which are remnants of mostly ancient viruses that snuck themselves into human genes during the course of evolution.

LINE-1 elements, also called selfish elements, can pop around the human genome and produce reverse transcriptase when activated.

Unlike retroviruses like HIV, SARS-CoV-2 does not carry a reverse transcriptase enzyme that helps it transcribe back into DNA, but these LINE-1 elements could be doing the job, according to Jaenisch. Taken together, he says these results provide proof that the mechanism of integration involves these LINE-1 elements.

“We proved beyond doubt that this is the mechanism,” he told MedPage Today. “It is possible that this reflects a general biological process not specific to coronavirus.”

The Debate Continues

Viral integration has been described in many other viral infections, such as hepatitis C, influenza, and measles, and has been explored for its role in oncogenesis as with the human papillomavirus. But this study would be the first to show that a coronavirus can integrate into the human genome.

One of the preprints that argued against this idea was just published in the peer-reviewed Journal of Virology. The group of researchers from Purdue University, the University of Michigan, and the NIH, maintains that these viral-human chimeric transcripts are laboratory artifacts created during RNA sequencing.

“The new data show exceedingly low frequency events that could still be the result of statistical anomalies or inherent noise in the technology,” the authors wrote in an emailed statement to MedPage Today. “The current analysis does not really address the fundamental issue raised by many, and is insufficient to conclude any viral integration in COVID-19.”

Cedric Feschotte, PhD, of Cornell University, an original critic of the work, also remains skeptical and says that more research is needed to prove viral integration. However, he now acknowledges that the hypothesis is plausible.

“My main criticism is that, even if these chimeric transcripts are biologically real, they don’t require integration to occur,” he said. “There are other known mechanisms that can lead to the formation of chimeric transcripts during viral infection in the absence of integration.”

But the “greatest weakness” lies in not quantifying the frequency of these reported SARS-CoV-2 integration events. The LINE-1 mechanism has already been found to be involved in integration for other viruses. Scientists who are familiar with this process would expect that this could be the case, he added.

“The surprise would be not finding any integration at all in this experimental setting. The major question is the frequency: how much and how often. This study leaves us without a very clear picture of the frequency. It doesn’t tell me much that I didn’t know before,” he said.

On the other hand, Nobel laureate David Baltimore, PhD, a professor emeritus at Caltech, said that the results “look pretty convincing.”

“It looks to me like the results are pretty clear-cut. There are always people who hold out against a new finding, and we have to live with that,” Baltimore told MedPage Today. “It really looks like bits of genetic information from any RNA virus could be reverse transcribed and integrated into human genes. That may happen with the common cold or whatever other viruses infect us.”

While more researchers have come around to the updated results, the debate will continue to evolve, and the scientific community will be watching closely.

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