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New Study Stokes Debate: Did Mass Vaccination Fuel New COVID Variants?
The authors of the peer-reviewed study said their findings “demonstrate the potential” for new approaches for detecting and treating COVID-19 that would be effective for all variants. Some scientists said the study also supports the theory that mass vaccination may have prolonged the pandemic.
by Michael Nevradakis, Ph.D.
July 15, 2025
Researchers who set out to examine how SARS-CoV-2, the virus responsible for COVID-19, evolved to evade the human immune system have inadvertently added fuel to the debate over whether mass vaccination may have prolonged the pandemic.
A peer-reviewed study, published this month in the journal Scientific Reports, hypothesized that SARS-CoV-2’s pathway to infecting humans shifted over time. Understanding that process will help scientists develop treatments for all future variants of the virus, the authors said.
Using public datasets consisting of blood and nasal samples from over 500 people, split into COVID-positive and control groups, the researchers found that the original strain of the SARS-CoV-2 and early variants “primarily affected pathways related to viral replication” — the process through which viruses insert their genetic material into host cells, co-opting those cells to create new viral particles.
These earlier strains of the virus led to more changes in gene expression — the process through which cells convert instructions in our DNA into a functional product, such as a protein. This, in turn, led to more severe COVID-19 infections.
However, later strains of SARS-CoV-2, such as Beta and Omicron, “showed a strategic shift toward modulating and evading the host immune response,” but also resulted in milder infections for most people.
According to TrialSite News, this is a “striking evolutionary shift in how SARS-CoV-2 interacts with the human body,” suggesting that newer variants “may be optimized for immune evasion.”
Did mass COVID vaccination lead to development of new variants?
The study’s authors said their findings “demonstrate the potential” for new approaches for detecting and treating COVID-19 that would be effective for all variants.
The researchers identified 37 genes common to all SARS-CoV-2 variants. They noted that the virus, regardless of variant, consistently affected the same sets of genes in humans, acting as “a unifying thread through the pandemic’s viral diversity,” according to TrialSite News.
The study did not analyze the potential impact of COVID-19 vaccination on the immune response to SARS-CoV-2.
Yet, some scientists said the results show that the COVID-19 vaccines contributed to the evolution of SARS-CoV-2 and potentially exacerbated the pandemic.
However, Karl Jablonowski, Ph.D., senior research scientist for Children’s Health Defense, disagreed. He said:
“Judging by the results of the paper, it is unlikely the differences in gene expression of the infected are a result of evolutionary changes in the virus due to the vaccine. The changes begin to happen in the Beta variant, a variant that emerged before the onset of vaccinations.”
But according to investigative journalist Sonia Elijah, “It is noteworthy that Omicron’s emergence coincided exactly with widespread vaccination and the onset of booster campaigns in late 2021.”
Independent vaccine research consultant Geert Vanden Bossche, DVM, Ph.D., agreed. In a post on X last week, he said SARS-CoV-2 “blew through the 1st line of immune defense in large cohorts of C-19 [COVID-19] vaccinees.”
According to
Vanden Bossche, many vaccinated people experienced antibody-dependent enhancement of infection (ADEI), a process in which antibodies increase a virus’s ability to enter cells instead of protecting them, resulting in a more severe infection.
Vanden Bossche is a former senior program officer for vaccine discovery at the Gates Foundation and author of “The Inescapable Immune Escape Pandemic.”
He told The Defender that ADEI “is pronounced” in people with high antibody titers — a high level of COVID-19 antibodies in people with “diminished or poor neutralizing capacity” toward different COVID-19 variants. He said this includes “boosted COVID-19 vaccinees, but also nonvaccinated folks who recovered from severe disease.”
Through this process, the COVID-19 vaccines led to vaccine breakthrough infections — where people are infected with the disease they are vaccinated against — and immune focusing, where the body produces protective antibodies that target only specific parts of the pathogen, such as the COVID-19 spike protein,
Vanden Bossche said.
In August 2021, during the outbreak of the Delta variant and just months after the mass COVID-19 vaccination campaign began in most countries, Israel was seeing breakthrough infections occurring in 50% of those who tested positive for COVID-19, said Dr. Sharon Alroy-Preis, director of Israel’s Public Health Services.
In 2022, amid the emergence of the Omicron variant, theoretical physicist Josh Mitteldorf, Ph.D., raised the possibility that vaccinated populations “put intense selection pressure on the virus to evade the vaccine by mutating its spike protein, which is the only part of the virus to which vaccinated individuals have immunity.”
Immune focusing, in turn, “enables continued adaptive immune escape,” Vanden Bossche wrote, referring to the ability of pathogens to avoid being targeted by the host’s immune system.
“I believe Dr. Vanden Bossche’s arguments align with this study’s findings that variants like Omicron have evolved to evade vaccine-induced immunity, as evidenced by their ability to infect vaccinated individuals,” Elijah said.
TrialSite News wrote, “This shift coincides temporally with global vaccination campaigns.”
Previous studies also found COVID vaccines may have helped virus mutate
In 2021, Scientific Reports published a peer-reviewed article suggesting that vaccinated people may play a key role in helping SARS-CoV-2 variants evolve into variants that evade existing COVID-19 vaccines.
That study showed that the highest risk for establishing a resistant strain occurs when a large fraction of the population has been vaccinated, but the transmission is not controlled.
Earlier in 2021, the Centers for Disease Control and Prevention published a study showing that vaccinated people may transmit the Delta variant just as easily as the unvaccinated.
Regardless of the mechanisms through which SARS-CoV-2 evolved, Jablonowski said the virus has changed into an endemic coronavirus with mild symptoms. He said:
“One possible interpretation of the results is that the SARS-CoV-2 virus evolutionary trajectory is one that takes a direction towards mild symptoms, which minimizes the immune response against it and therefore increases transmissibility. We may one day refer to it as ‘the common cold.’”
