Monitoring chronic coronavirus infections may help forecast new variant threats, study suggests
CBC
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As Omicron began its swift spread around the world, theories about its origins sprang up as well.
Did the heavily mutated coronavirus variant evolve within an animal host before spilling back into humans or in a COVID-19 patient being treated with a drug capable of spurring viral mutations?
Or, many scientists wondered, did the latest variant of concern develop during a protracted battle against the virus inside the body of someone with a compromised immune system?
While there are no clear answers just yet to the questions around Omicron's emergence, that third theory — tied to viral evolution inside immunocompromised hosts — is an area that's getting attention from researchers, with one new study suggesting that monitoring chronic infections may be a means to predict future variants that could pose a threat.
In early findings, published online as a preprint paper and not yet peer-reviewed, a team of Israeli researchers affiliated with Tel Aviv University looked at 27 chronically infected coronavirus patients.
All of those individuals had suppressed immune systems for various reasons, including certain cancers, high-dosage steroid treatment or low levels of T-cells from conditions such as AIDS.
"Presumably, these immune system disorders prevent clearance of the virus as compared to patients with an intact immune system, and thus the virus thrives for lengthy periods of time," the researchers wrote.
Typically during SARS-CoV-2 infections, viral shedding lasts anywhere from a few days to a few weeks.
But documented cases of chronic infections, such as those studied by the team, can last far longer, with replicating viruses detectable for lengthy periods of time. (That's notably different from long COVID, the researchers noted, in which the initial infection is shorter but symptoms persist.)
After analyzing the set of patients with chronic infections, the team concluded that the overall patterns of mutations observed in those cases "closely mirror" the patterns observed in variants of concern.
There were instances of viral rebound, for example, where the virus dropped to undetectable levels but then appeared to replicate throughout the body again — which may suggest mutations capable of evading antibodies, the researchers wrote, offering a possible signal that scientists can use to identify future variants.
But in their small sample of patients, the team didn't find instances of certain mutations that could drive virus transmission, prompting researchers to suggest that any variants emerging in chronically infected patients might lack that key capability. That's a potential trade-off, they argued, between the virus becoming more transmissible or more immune evasive.
"Overall, we suggest that extensive monitoring of chronic infections can be used for forecasting the set of mutations in future [variants of concern]," the team concluded.