The pandemic coronavirus SARS-CoV-2 (pictured above) can, under certain circumstances, integrate its genetic material into human cells, interfering with COVID-19 diagnostic tests.
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By Jon Cohen
Science‘s COVID-19 reporting is supported by the Pulitzer Center and the Heising-Simons Foundation.
People recovering from COVID-19 sometimes test positive for SARS-CoV-2 later, suggesting that their immune system is unable to ward off a second attack by the coronavirus or that they have an ongoing infection. A study now points to another explanation in which the virus is hiding in an unexpected place. The work, reported only in a preprint, suggests that the pandemic pathogen takes a page from HIV and other retroviruses and integrates its genetic code – but more importantly, only parts of it – into the chromosomes of humans. If the phenomenon is true and frequent, it can have profound implications ranging from false signals of active infection to misleading results from COVID-19 treatment studies.
The current study only showed this integration in a lab scale, although it also cites published sequence data from people infected with SARS-CoV-2 suggesting it happened. The authors emphasize that their results do not imply that SARS-CoV-2 establishes a permanent genetic residence in human cells to keep pumping new copies, as HIV does.
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Other scientists are divided on the importance of the new work and its relevance to human health, and some are very critical. “There are open questions we need to answer,” said molecular biologist Rudolf Jaenisch of the Massachusetts Institute of Technology (MIT), who led the work.
Still, a few experienced retrovirologists are fascinated. “This is a very interesting molecular analysis and speculation with supporting data,” said Robert Gallo, head of the Institute of Human Virology, reviewing the newly posted preprint on Science‘s request. “I don’t think it’s a complete story to be sure … but as it is, I like it and I suspect it will be fine.”
All viruses transfer their genetic material into the cells they infect, but it generally remains separate from the cell’s own DNA. Jaenisch’s team, intrigued by reports from people who tested positive for SARS-CoV-2 after recovery, wondered if these puzzling results reflected some artifact of the polymerase chain reaction (PCR) test, which detects specific virus sequences in biological samples such as nasal swabs, even if they are fragmented and cannot produce new viruses. “Why do we have this positivity, which is everywhere now, long after the active infection has disappeared?” says Jaenisch, who worked with MIT’s Richard Young lab.
To test whether the RNA genome of SARS-CoV-2 can be integrated into the DNA of our chromosomes, the researchers added the gene for reverse transcriptase (RT), an enzyme that converts RNA into DNA, to human cells and engineered cells grown with SARS-CoV-2. In one experiment, the researchers used an HIV RT gene. They also delivered RT using human DNA sequences known as LINE-1 elements, which are remnants of old retroviral infections and make up about 17% of the human genome. Cells that made both forms of the enzyme resulted in some pieces of SARS-CoV-2 RNA being converted into DNA and integrated into human chromosomes, the team reports in their printout, which was posted on bioRxiv Dec. 13.
If the LINE-1 sequences naturally make RT in human cells, SARS-CoV-2 integration can occur in humans with COVID-19. This can also occur in people co-infected with SARS-CoV-2 and HIV. Both situations may explain why PCR detects persistent traces of coronavirus genetic material in people who no longer have a true infection. And it could confuse studies of COVID-19 treatments that rely on PCR testing to indirectly measure changes in the amount of infectious SARS-CoV-2 in the body.
David Baltimore, a virologist at the California Institute of Technology who won the Nobel Prize for his role in discovering RT, describes the new work as “ impressive ” and the findings as “ unexpected, ” but notes that Jaenisch and colleagues leave alone. see that fragments of the genome of SARS-CoV-2 integrate. “Because they are all pieces of the coronaviral genome, it cannot lead to infectious RNA or DNA and is therefore likely to be a biological dead end,” says Baltimore. “It is also not clear whether in humans the cells harboring the reverse transcripts persist for a long time or whether they die. The work raises many interesting questions. “
Virologist Melanie Ott, who studies HIV at the Gladstone Institute of Virology and Immunology, says the findings are “quite provocative,” but need thorough follow-up and confirmation. “I have no doubt that reverse transcription can be done in vitro under optimal conditions,” said Ott. But she notes that SARS-CoV-2 RNA replication takes place in specialized compartments in the cytoplasm. “Whether it happens in infected cells and … leads to significant integration into the cell nucleus is another question.”
Tufts University retrovirologist John Coffin calls the new work “credible,” noting that solid evidence shows that LINE-1 can allow RT to integrate viral material into humans, but he is not convinced yet. The evidence of SARS-CoV-2 sequences in humans, Coffin says, “should be more robust,” and the in vitro experiments conducted by Jaenisch’s team lack controls he would have liked to see. “All in all, I doubt the phenomenon has much biological relevance, despite the authors’ speculation,” said Coffin.
Zandrea Ambrose, a retrovirologist at the University of Pittsburgh, adds that this kind of integration would be “extremely rare” if it did happen. She notes that LINE-1 elements in the human genome are rarely active. “It is not clear what the activity would be in different primary cell types infected with SARS-CoV-2,” she says.
a particularly harsh Twitter critic, a graduate student in a laboratory specializing in retroviruses, went so far as to call the preprint conclusions “a strong, dangerous and largely unsupported claim.” Jaenisch emphasizes that the paper clearly indicates that the integration that the authors say is taking place cannot lead to the production of infectious SARS-CoV-2. “Let’s assume we can really resolve this criticism completely, which I am trying to do,” Jaenisch says. “This might not be something to worry about.”