The science of why some people test positive for COVID-19 longer than others.
“Don’t tell me I have COVID again,” says a flabbergasted Nick Riley, a Boston-based production member whose name has been changed to protect his identity. “I got it bad back in December: fever, loss of smell, the whole nine yards. To be honest with you, I would be surprised if this wasn’t a false positive. I really would. I feel a hundred percent [healthy] right now.” Like many in Massachusetts, Riley contracted COVID-19 early in the Omicron surge, before weekly cases reached 2,510 per 100,000 residents. Despite the possibility that his most recent positive result is a new asymptomatic breakthrough case, he would not be the first person to continue to test positive on PCR tests months after his initial infection without any indication of active, replicating, virus. With the surge in Omicron cases came an increase in a strange, albeit rare, phenomenon that has stumped scientists and clinicians alike: the case of the persistent positive.
“Maybe there’s something else, other than replicating virus, which could give rise to PCR positive signal,” says Dr. Rudolph Jaenisch, professor of biology at the Massachusetts Institute of Technology (MIT) and founding member of the world-renowned Whitehead Institute. “That [question] is what really prompted our hypothesis and our study.” Jaenisch and his team at the Whitehead Institute are among the scientists spearheading research into this phenomenon. In a recently published study in the Proceedings of the National Academy of Science (PNAS), Jaenisch and his team have persuasively demonstrated that SARS-CoV-2, the virus that causes COVID-19, can integrate “bits and pieces” of its genes into the genome of human cells in rare instances called host-virus “chimeric events”.
Chimeric events borrow their name from the chimera, an awkward creature of Greek mythology that cobbles together a lion, snake and fire-breathing goat into one body (a Hollywoodized version of which can be seen in 2012’s Wrath of the Titans). Similarly, in science, “chimeric events” refer to cases of two organisms infusing together. These events occur mostly between humans and viruses (though it has been known to occur between twins) at a genetic level where genes from a virus become integrated into human DNA. Certain types of viruses, such as retroviruses, do this naturally as a compulsory part of replicating themselves. Jaenisch, who has spent much of his impressive career studying retroviruses, says it’s knowledge of this phenomenon that inspired his hypothesis. The one problem? The coronavirus is not a retrovirus, so how the heck did it integrate? The answer, you’ll find, is stranger than mythology.
The Strange World of Viruses
Given the variety of life on earth, it might surprise you that viruses are not considered “alive” per se, like big cats or bacteria. In fact, viruses are less like the living and more like incomplete blueprints of them. Indeed, it’s best to think of viruses as independent genes that dance about our environment “tugging along pieces of this genome, strings of genes from that, transplanting grafts of DNA, passing around heredity as though at a great party,” as biologist Lewis Thomas put it in Lives of a Cell. And, just like the genes in your cells that divide into new cells, viruses are always trying to replicate and create new viruses, only they don’t have the ability to do so on their own. Instead, they use a crown of “keys” called antigenic determinants to jimmy the lock on the doors into our cells and inject their genetic material into the cell. Once inside, the virus hijacks the cell’s machinery, and, in some cases, inserts their genetic material into a host’s DNA. Certain types of viruses, known as retroviruses, accomplish this through a molecular tool known as reverse transcriptase.
To better understand the role of reverse transcriptase, let’s think about film scripts for a moment. Every English scriptwriter, from Shakespeare to Spike Lee, has written their scenes using the same 26 letter alphabet. With just 26 letters, Jack Dawson lived and died, King Kong climbed the Empire State Building, and Chazz Reinhold from Wedding Crashers yelled “Ma, THE MEATLOAF!” Similarly, every person that has ever existed, from Ghengis Khan to Goldie Hawn, has been written with DNA using just four nucleotide bases known as adenine (A), cytosine (C), guanine (G) and thymine (T). To turn those four letters into petals and pupils, cell walls and cerebrums, takes cellular foremen who can transcribe the blueprint of life and translate it into works of biological architecture. In biology, we call these foremen RNA. Almost every form of life, from geraniums to Jeff Goldblum, are written with just those 4 letters; all except for some types of viruses. Rather than the familiar A, C, G, T alphabet of DNA, some types of viruses use an A, C, G, U (Uracil) alphabet called RNA as the basis of their blueprint. In order to reproduce themselves, they must transcribe the language of RNA into the language of DNA. Just as we might use Google Translate to transcribe English into Russian, reverse transcriptase transcribes RNA into DNA. Viruses, such as retroviruses, then insert this DNA into animal genomes in order to produce new viruses. What is strange, however, is that while retroviruses integrate their genome as a necessary step of their replication cycle, RNA viruses like coronavirus do not. But how could that be? The answer to this question reveals a strange similarity between viruses and our very own genes.
The Amazing Jumping Genes
As it turns out, we too have sequences of DNA that code for this tool, reverse transcriptase. Some of these genetic sequences are the result of ancient viruses integrating with our genome millions of years ago while other sequences arose independently through changes in our evolution. Scientists have shown that, sometimes, certain types of human reverse transcriptase will accidentally integrate bits and pieces of viral genes into our DNA. Dr. Jaenisch and his team have shown that, with coronavirus, this appears to be the case.
In 2003, scientists internationally celebrated the completion of the Human Genome Project, a monumental and colossal scientific undertaking to identify and map the landscape of the human genome (all made possible through the PCR technique most known for COVID-19 testing). What the scientists found was surprising: a whopping 45 percent of the genome was made up of sequences of DNA that behave in a very peculiar way: they “jump” around your genome. “Jumping genes”, also known as transposons, shift positions within our DNA, providing a variety of essential services. Of these 45 percent of transposons, the majority are known as retrotransposons; and, much like the retroviruses we saw above, they use reverse transcriptase to duplicate a sequence of their genetic code and insert the new strand into your genome. About 8 percent of these retrotransposons are the remnants of ancient retroviruses that integrated with our ancestor’s genomes over 25 million years of evolution. (Some of them are even to our benefit! Ever enjoy a delicious basket of french fries? Well, you can thank an ancient virus for our ability to digest starch.) The rest, however, are similar in function, but unrelated to retroviruses; they make up about 17 percent of the genome and include important segments of code known as Line1, long thought to be “junk DNA”.
This is where Dr. Jaenisch’s work comes in. Jaenisch’s lab has shown that Line1 segments are able to trans-integrate sequences of code from viruses such as the coronavirus into the DNA of cells. “We are sure about this because line1 integration leaves footprints very specific for line1,” he tells me. Because Line1 encodes reverse transcriptase (that Google-Translate-like molecular tool), it’s able to transcribe the coronavirus’s RNA into DNA that can then be integrated into the DNA in human cells, such as those in the respiratory tract. This is thought to be one explanation for why people continue to test positive months after an initial COVID-19 infection. “Some cell types survive the infection for a much longer time than other cell types. Those in the nose could give rise to PCR positivity long after the infectious virus has disappeared. In that way it was consistent with our hypothesis,” says Dr. Jaenisch.
While research is still underway, the data from Dr. Jaenisch et al has provided a tantalizing and persuasive explanation for the persistent positive. If virus-host chimeric events are truly the cause for persistent positive PCR signals, this may add some value to the use of antigen tests for diagnosing COVID-19. This is because PCR and antigen tests target different parts of the virus’s anatomy. PCR assays test for the genetic sequences while antigen tests target the crown of proteins on the outer shell of the virus. While this distinction may be useful in the diagnosis of COVID-19, it does not mean that antigen tests are a better tool. Antigen tests are still less sensitive than PCR tests meaning they have a higher rate of false negative results. Rather, antigen tests are an important supplemental tool for healthcare providers to use in diagnosis and ought to be used in tandem with other indicators such as CT values, history of infection, and current symptoms. This is why if you find yourself with a positive COVID-19 result it is always best to consult your physician, even if you think it is a false or persistent positive.
Should you be worried about chimeric events?
If you have tested positive after recovering from a COVID-19 infection, should you be worried about this phenomenon? Dr. Jaenisch says, probably not. While, understandably, chimeric events sound unnerving, there is little evidence to suggest there are any negative effects, though, he speculates it could be one explanation for long-haul COVID-19 symptoms. The high frequency of COVID symptoms after even mild infections, particularly autoimmune symptoms, has Jaenisch somewhat worried. “Could integration explain that?” he wonders. “If we know the integrated sequences become expressed to make RNA, the real question is can they make antigen? Can they get translated, bits and pieces?” Jaenisch emphasizes that this is mere speculation and there is no current data to suggest this is the case. But if it were true, this could cause the immune system to attack healthy cells, resulting in an autoimmune disease.
On the flip side, chimeric events may also lead to a more robust immunity to the virus. Jaenisch’s team has not ruled this out. By the same token, long term exposure to antigen fragments produced by the “bits and pieces” of integrated genes could, hypothetically, prepare your immune system to better defend against subsequent encounters with the virus.
As it stands now, though, integration is extremely rare. “In patients we believe the integration is so rare, maybe one in ten-thousand, maybe less in the cell, that you cannot find direct evidence for DNA integration,” says Dr. Jaenisch. Through ingenious indirect means, Jaenisch and his team at the Whitehead Institute, have confirmed that chimeric events with the coronavirus can occur without a doubt. What is of greater importance is that these chimeric events don’t appear to be passed down through generations. While some viruses, such as ebola, can make changes to the genome that are passed down to subsequent generations, it does not appear that coronavirus can do so.
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