What Is Causing All These New Coronavirus Variants? Is It the COVID–19 Vaccines?

Coronavirus Genetic Mutation Concept

The huge number of active coronavirus infections offers plenty of opportunity for mutations to occur and new variants to arise.

Massive numbers of new COVID–19 infections are the main driver of new coronavirus variants.

The rise of coronavirus variants has highlighted the huge influence evolutionary biology has on daily life. But how mutations, random chance and natural selection produce variants is a complicated process, and there has been a lot of confusion about how and why new variants emerge.

Until recently, the most famous example of rapid evolution was the story of the peppered moth. In the mid-1800s, factories in Manchester, England, began covering the moth’s habitat in soot, and the moth’s normal white coloring made them visible to predators. But some moths had a mutation that made them darker. Since they were better camouflaged in their new world, they could evade predators and reproduce more than their white counterparts.

We are an evolutionary biologist and an infectious disease epidemiologist at the University of Pittsburgh who work together to track and control the evolution of pathogens. Over the past year and half, we’ve been closely following how the coronavirus has acquired different mutations around the world.

It’s natural to wonder if highly effective COVID-19 vaccines are leading to the emergence of variants that evade the vaccine – like dark peppered moths evaded birds that hunted them. But with just under 40% of people in the world having received a dose of a vaccine – only 2% in low-income countries – and nearly a million new infections occurring globally every day, the emergence of new, more contagious variants, like delta, is being driven by uncontrolled transmission, not vaccines.

Coronaviruses RNA Genetic Code

Coronaviruses use RNA to store information, and small changes in that genetic code can lead to new strains of the virus.

How a virus mutates

For any organism, including a virus, copying its genetic code is the essence of reproduction – but this process is often imperfect. Coronaviruses use RNA for their genetic information, and copying RNA is more error-prone than using DNA. Researchers have shown that when the coronavirus replicates, around 3% of new virus copies have a new, random error, otherwise known as a mutation.

Each infection produces millions of viruses within a person’s body, leading to many mutated coronaviruses. However, the number of mutated viruses is dwarfed by the much larger number of viruses that are the same as the strain that started the infection.

Nearly all of the mutations that occur are harmless glitches that don’t change how the virus works – and others in fact harm the virus. Some small fraction of changes may make the virus more infectious, but these mutants must also be lucky. To give rise to a new variant, it must successfully jump to a new person and replicate many copies.

Transmission Bottleneck New Variants

The bottleneck of transmission is what limits the ability of a new variant to infect another person. Credit: Vaughn Cooper via Biorender, CC BY-ND

Transmission is the important bottleneck

Most viruses in an infected person are genetically identical to the strain that started the infection. It is much more likely that one of these copies – not a rare mutation – gets passed on to someone else. Research has shown that almost no mutated viruses are transmitted from their original host to another person.

And even if a new mutant causes an infection, the mutant viruses are usually outnumbered by non-mutant viruses in the new host and aren’t usually transmitted to the next person.

The small odds of a mutant being transmitted is called the “population bottleneck.” The fact that it is only a small number of the viruses that start the next infection is the critical, random factor that limits the probability that new variants will arise. The birth of every new variant is a chance event involving a copying error and an unlikely transmission event. Out of the millions of coronavirus copies in an infected person, the odds are remote that a fitter mutant is among the few that spread to another person and become amplified into a new variant.

B.1.1.7. SARS-CoV-2 Coronavirus Variant

Mutations have changed the structure of the spike protein, seen in red, and made the coronavirus better able to infect cells using the ACE2 receptor, seen in blue. Credit: Juan Gaertner/Science Photo Library

How do new variants emerge?

Unfortunately, the uncontrolled spread of a virus can overcome even the tightest bottlenecks. While most mutations have no effect on the virus, some can and have increased how contagious the coronavirus is. If a fast-spreading strain is able to cause a large number of COVID-19 cases somewhere, it will start to out-compete less contagious strains and generate a new variant – just like the delta variant did.

Many researchers are studying which mutations lead to more transmissible versions of the coronavirus. It turns out that variants have tended to have many of the same mutations that increase the amount of virus an infected person produces. With more than a million new infections occurring every day and billions of people still unvaccinated, susceptible hosts are rarely in short supply. So, natural selection will favor mutations that can exploit all these unvaccinated people and make the coronavirus more transmissible.

Under these circumstances, the best way to constrain the evolution of the coronavirus is to reduce the number of infections.

Vaccines stop new variants

The delta variant has spread around the globe, and the next variants are already on the rise. If the goal is to limit infections, vaccines are the answer.

Even though vaccinated people can still get infected with the delta variant, they tend to experience shorter, milder infections than unvaccinated individuals. This greatly reduces the chances of any mutated virus – either one that makes the virus more transmissible or one that could allow it to get past immunity from vaccines – from jumping from one person to another.

Eventually, when nearly everyone has some immunity to the coronavirus from vaccination, viruses that break through this immunity could gain a competitive advantage over other strains. It is theoretically possible that in this situation, natural selection will lead to variants that can infect and cause serious disease in vaccinated people. However, these mutants must still escape the population bottleneck.

For now, it is unlikely that vaccine-induced immunity will be the major player in variant emergence because there are lots of new infections occurring. It’s simply a numbers game. The modest benefit the virus would get from vaccine evasion is dwarfed by the vast opportunities to infect unvaccinated people.

The world has already witnessed the relationship between the number of infections and the rise of mutants. The coronavirus remained essentially unchanged for months until the pandemic got out of control. With relatively few infections, the genetic code had limited opportunities to mutate. But as infection clusters exploded, the virus rolled the dice millions of times and some mutations produced fitter mutants.

The best way to stop new variants is to stop their spread, and the answer to that is vaccination.

Written by:

  • Vaughn Cooper – Professor of Microbiology and Molecular Genetics, University of Pittsburgh
  • Lee Harrison – Professor of Epidemiology, Medicine, and Infectious Diseases and Microbiology, University of Pittsburgh

This article was first published in The Conversation.The Conversation

20 Comments on "What Is Causing All These New Coronavirus Variants? Is It the COVID–19 Vaccines?"

  1. EXACTLY!

    Just like all those people NOT taking antibiotics contributing to antibiotic resistance!

    EVERYBODY should be on antibiotics FOREVER to ensure we don’t have antibiotic resistant strains!

    …oh wait… that (like this article) is COMPLETE BS!

    • Viruses and Bacteria are not the same. For starters Viruses are made with RNA and Bacteria are made with DNA. They don’t compare in the slightest. But thank you for proving you don’t know basic biology. 🙂

      • Covid vaccines are by definition a “leaky vaccine” and leaky vaccines can cause viruses to mutate into stronger versions of itself making it more deadly and more contagious. Sound familiar? Marek’s disease is the first and only study of this kind and we are just beginning to understand how vaccines can make viruses more deadly.I’m sure you are aware of this inconvenient truth and so is the author.

        • History doesn’t prove exceptions.
          It only notes them.

          The first influenza vaccine for the public was offered in 1945.
          It’s constantly being updated to address mutations.
          And yet, the worst influenza pandemic in recent history was before a vaccine was available. That would be 1918.
          Yes, inconvenient truths are indeed inconvenient.

      • Correction.
        There are DNA viruses.

        https://www.rxlist.com/dna_virus/definition.htm

        But as you posted, they don’t compare well.

    • This article explains the processes that you apparently don’t understand. You should read it again, or have someone who doesn’t have a reading comprehension deficit read it and explain it to you.

    • @theCnner

      I’ll consider the claims of two knowledgeable scientists:
      https://scholar.google.com/citations?user=dcezvIQAAAAJ&hl=en&oi=ao
      and
      https://scholar.google.com/citations?user=v88WxTwAAAAJ&hl=en&oi=ao
      before some know-nothing poster with reading comprehension issues that only knows how to berate common sense, logic and science.

      To the authors of the article, thank you for an understandable explanation.

    • Antibiotics and vaccines are conceptually different processes.
      Antibiotics kill, vaccines create immunity.

      Your post and it’s conclusion is worthless.

  2. viruses work differently than bacteria, yes, but its the same principle. lets say you have a vaccine for a virus that has a ever changing RNa sequence, so you get one vaccine, but the virus is able to mutate with another virus and change the way that it affects but not attacks, sounds kind of like the flu huh.

    • The Covid-19 vaccine does not attack and destroy the virus leaving the ‘fittest’ to survive and replicate. It blocks the ACE2 receptor from accepting a specific viral infection.
      It takes a different means of attack derived from a mutation, in order to infect.
      How it affects after infection depends on what other mutations also occurred.
      The greater the number of infections, the greater the risk of possible viable mutations.

  3. Wow, the headline of this article is so misleading and irresponsible. It should read “What Is Causing All These New Coronavirus Variants? It’s NOT the COVID–19 Vaccines.”

  4. A 90% effective vaccine is not better than a P100% mask and goggles forming a physical barrier to infection and reinfection and mutation, unless one is too stupid / arrogant / vain to properly use a proper mask. The mere fact that a vaccinated person can be an asymptomatic carrier demonstrates that a mutating virus can only be stopped by physical barries, not “pricks.”

    Then there is the issue of big-pharma profiteering by concealment that Probenecid is an FDA-approved medication primarily used to treat gout, with few side effects — effective on all RNA respiratory viruses, including SARS-CoV-2. DOI: 10.1038/s41598-021-97658-w

    • Your mask argument is a fallacy.
      Vaccines, in general, have shown reductions in transmission.
      They’ve been very effective with childhood diseases.

      You are arguing for perfection as a means to discredit medical science.

      And about ‘Probenecid’. It’s been reported the lead author holds a University position in veterinary science and his live tests have been with hamsters.
      It’s also been reported testing is being conducted by ‘others’.
      In a human, it does make a person pee out uric acid a lot faster.

  5. “…more contagious variants, like delta, is being driven by uncontrolled transmission, not vaccines.”

    I am going to disagree on this. It is still possible to get infected and transmit the virus, even with the vaccine. Events and gatherings in USA are only testing unvaccinated people. Leaving vaccinated people as asymptomatic carriers, encouraging virus to mutate

  6. It is far more likely that the non-vaxxers are providing the environment for the covid variants to evolve. That is why those variants came from countries that did not have enough vaccines or a distribution system.

  7. Israel numbers…

  8. Howard Jeffrey Bender, Ph.D. | September 14, 2021 at 3:55 pm | Reply

    Stopping new variants with new vaccines is great for the vaccine companies, but is a losing battle for the rest of us.

    All the coronaviruses and all their variants have different protein spikes, with Delta having one that’s more efficient at getting around the vaccines. But the real problem is in the virus itself, not its protein shell, and why the most dangerous (MERS, SARS, and Covid-19) are so infectious. My independent research has found multiple one-in-a-million nucleotide sequence matches between all the coronaviruses and the human genome. Those sequences are the same as some of the loops of human tRNA. Using those loops and their amino acid code matches, viruses may be able to fool the nucleus membrane in cells to allow the virus to enter and associate with the human DNA, creating more opportunities for further infection. Our immune system may be compromised and may no longer be able to stop the virus and other diseases from attacking organs throughout the body. Vaccines that attack the virus protein shells while ignoring their contents are doomed to failure from the Darwin effect, but recognizing these loops suggests a possible approach to successful coronavirus vaccines. Only the infection process is considered in my work, not the innate virulence of the virus. For more info, check out this YouTube, Coronavirus – Using Your DNA Against You. https://www.youtube.com/watch?v=8dOIzD6ch8s

  9. Where to begin… of course these mRNA therapies are causing the variants AND and at a much more rapid and infectious pace. With millions getting these shots, those persons’ immune systems are becoming more and more alike; the more alike, the easier it is for the virus to adjust. Never before in Nature has this happened! Our built-in diversity is what protects the human population; if we were all alike, we would all be dead! Chaos is our friend.

    And this is just speaking to the virus variants; the Pandora’s Box of “unintended consequences” is an entirely different concern. The speed to in which people’s immune systems are being modified is magnitudes faster than how it occurs naturally. So now, our bodies will be fighting our bodies; no winner in that conflict.

    I pray I’m wrong.

  10. ALready proven that vaccinated people carry viral loads as high or 250x higher than non vaccinated in UK, Singapore, Vietnam and Massachusets. Vaccines do pressure mutations because antibodies are against the S protein which is the part that is trying to mutate.

  11. So, here we are almost a month later. We have a “booster” coming out.
    And even a yearly flu vaccine.
    When will this end?
    I enjoyed reading this article and the comments as well.
    Thank you for sharing this information
    Our lives depend on truth and understanding

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