A 60-year-old woman spent more than seven months testing positive for Covid-19, during which time she developed 22 Sars-CoV-2 coronavirus mutations. The case was reported by an Austrian virologist, who followed up on the patient.
An elderly woman infected in late 2020 was taking immunosuppressive drugs to treat recurrence of lymphoma before Covid-19. During the period of contamination, he had mild symptoms of the disease, such as coughing and fatigue.
At the Ausservillgraten microbiology facility, the researcher and his colleagues analyzed more than 24 viral samples from residents. Mutations observed in half of these were also detected in the Ômicron variant, which emerged in late 2021.
“When they found Omicron, we had a big surprise moment,” Sissy Therese Sonnleitner told Nature magazine. He added: “We already had these mutations in our variant.”
This variant did not originate from the woman’s infection and, according to the virologist, did not transmit it to anyone. However, although not yet fully proven, chronic infections — such as those of the patient — are the main candidates for the origins of Omicron and other variants that drove Covid-19 waves worldwide.
“I don’t think anyone can doubt that [infecções longas] they are a source of new variation, ”added Cambridge University virologist Ravindra Gupta to Nature.
Since the end of 2019, scientists have sequenced the genomes of more than 11 million samples of Sars-CoV-2 samples taken from patients. This action led to the drawing of an evolutionary tree of the virus, which shows how it has changed in every passage on the planet. Only a few mutations were stable because they were transmitted to other people for more than a month.
According to the study, new mutations occur as the infection spreads from cell to cell. Not all of them will be harmful, but there are those that can add benefits to other versions of the virus in the individual’s body, increasing their ability to infect or offering greater resistance to immune defenses.
These two situations are the main evolution of Sars-CoV-2 since its discovery in 2019.
In acute infections that last for about a week or two, “advantageous” mutations have less time to overcome the weaker ones, which in theory has a low chance of transmission.
However, research shows that only a few virus particles are needed, perhaps only one, to create a new infection. Therefore, the possibility of contamination ends up becoming uncertain.
“One of those viruses in the aerosol droplets that makes you sneeze the moment someone passes by and breathes is largely a matter of luck,” Jesse Bloom, an evolutionary biologist at the Fred Hutchinson Cancer Center in Seattle, told Nature.
In chronic infections, which can last for weeks or months, viruses with “advantageous” mutations have more time to outperform others. In a process called recombination, which involves combining the genetic material of two strains, more suitable viruses may appear.
“These viruses have the potential not only to evolve in one way or another, but literally thousands, perhaps tens of thousands of directions over the course of months,” said Sarah Otto, an evolutionary biologist at the University of British Columbia.
Find the source of the variants
The Alpha variant, identified in the UK at the end of 2020, was the first variant of Sars-CoV-2 suspected to have originated from a chronic infection. But it is not the only hypothesis that it may have originated in a region with little capacity for genomic surveillance.
Andrew Rambaut and Verity Hill, biologists at the Institute for Evolutionary Biology at the University of Edinburgh, suggest that it may have been a possible source of chronic infection. The discovery of an intermediate version of Alpha, received by a person in the south-east of England in July 2020, two months before it was first detected in the same region, was announced in a pre-press release in March.
The virus had several characteristics of Alpha, and research suggests that it had a high ability to spread when it combined mutations only once.
These combinations have also been seen in Omicron, which overlaps several substrates and mutations. The lower severity of this variant may also be the result of a chronic infection, as research shows that this aspect was acquired as a result of the virus’s preference for infecting the upper respiratory tract.
It probably progressed from a strain that infected the upper and lower respiratory tract and from a coordinated evolution, when a virus spends months in a person’s body. However, it is not yet clear what evolutionary forces drove this change.
Researchers want to understand how the virus can evolve more easily from one person to another, escape the immune response, or become more or less severe. Chronic infections can provide all or some of these answers.
The chances that this knowledge will help prevent a coming deadly strain or trace the origin of a new variant are still far away.
But virologists hope that this contribution to understanding viral evolution can predict what future variants will look like and find effective ways to treat chronic infections, especially for people with immune deficiencies who do not always respond strongly to vaccines.
“It’s such a big problem that we don’t want another variant that we can’t deal with,” Alex Sigal, a birologist at the Africa Health Research Institute in Durban, South Africa, told Nature.
He added: “We need to go beyond case reports and understand what the virus is really evolving at this time.”