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Where Do Viruses Come From? (Read 24 times)

Jovial Monk

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Where Do Viruses Come From?
Dec 2^nd, 2025 at 11:21am

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Where Do Viruses Come From?

Using genomics, evolutionary biologists test several hypotheses on the origin of viruses. New evidence suggests they may have emerged more times than previously thought.

Scientists have put forward a bevy of theories to explain how each realm came into existence. However, new genome sequencing data is compelling virologists to rework virus family trees by splitting realms apart and rewriting the history of virus evolution.

Did Viruses Appear Before Cells?

To investigate the origins of viruses, scientists look back to the earliest stages of life on Earth. Even though all modern viruses rely on cells for their replication, one idea, known as the “virus-first hypothesis,” proposes that viruses appeared before cells came into existence.4 This scenario could apply to at least five of the seven viral realms that infect every domain of life. Take the Duplodnaviria realm, for example: Its DNA viruses are found in archaea, bacteria (as bacteriophages), and eukaryotes (including herpesviruses). Because these hosts are so fundamentally different, it’s unlikely that a virus infecting one could have simply evolved to infect another. This suggests that the ancestor of Duplodnaviria must have already existed by the time of LUCA or perhaps even earlier, lending support to the virus-first hypothesis.

Seems legit, but;
Quote:

Some viral realms infect only specific groups of organisms, which suggests they arose after certain branches of life had already evolved, rather than dating all the way back to LUCA. For instance, viruses in the Adnaviria realm are found exclusively in archaea, implying they likely emerged after archaea appeared around 3.8 billion years ago

Oops, not that clear!

Quote:

However, taking a closer look at viral proteins can cast doubt on that conclusion. For example, viruses in the Ribozyviria realm only infect eukaryotes, so it would seem logical that they evolved after eukaryotes emerged about 1.7 billion years ago. Yet, these viruses possess ribozymes—RNA-based enzymes—that trace their origins back to the ancient RNA world, hinting that they may be much older, possibly predating cellular life itself, Zerbini noted.

Corroborating the virus-first hypothesis is challenging. Tracing lineages back four billion years involves such large uncertainties that it’s impossible to tell which came first, the virus or the cell. To complicate matters further, scientists have found that every viral realm contains genes related to those in cellular DNA. This makes it hard to determine if viruses were precursors to cells, if they both arose independently and later exchanged genes—which both fit the virus-first model—or if viruses actually originated from cells. Regardless of the answer, viruses and cells have profoundly influenced each other’s evolution.

That last is very true.

Quote:

Viruses May Have Come from a Minimalist Cell
How could viruses, typically harboring only a handful of genes, have emerged from cells equipped with thousands of genes? The “reduction hypothesis” suggests that this could have happened if parasitic cells rid themselves of most of their genes and became dependent on other cells.4 Researchers know that bacterial pathogens like sexually-transmitted Chlamydia trachomatis and typhus-causing Rickettsia prowazekii have purged genes important for synthesizing biomolecules because they can just sequester those resources from their hosts.8

Since all viral realms contain a portion of genes homologous to cellular proteins, it seems likely that viruses emerged in the same way as obligate intracellular pathogenic bacteria—by reduction of a cellular genome, but to a more extreme extent. The discovery of giant viruses in the realm Varidnavira originally lent support to this theory.

“Giant viruses look like cells. They were confused with small bacteria at the beginning,” said Gustavo Caetano-Anollés, an evolutionary biologist at the University of Illinois Urbana-Champaign. Whereas most viruses contain hardly any genes (such as SARS-CoV-2, which caused the COVID-19 pandemic with merely 11 protein-coding genes), giant viruses carry thousands of genes. Many of them code for cellular factors like translation enzymes or ribosomal proteins, providing more evidence that they could have been reduced from cells. “I think they're a case for the reductionist hypothesis, actually, because maybe with a few more genes, they would become independent agents,” Zerbini said.

However, a study from 2023 challenged this view, finding that giant viruses probably emerged from smaller viruses instead.

Wow, talk about complex problem!

Quote:

Did Cell Components Escape to Become Viruses?
Genome reduction isn’t the only way that viruses could have emerged from cells. The “escape hypothesis” suggests that viruses could have emerged from a few cellular components that broke loose.4 Perhaps the most compelling evidence for this comes from the realm Riboviria, which contains retroviruses like human immunodeficiency virus (HIV). Retroviruses are RNA viruses that produce DNA copies of their genomes that they insert into host DNA. It is possible that these arose from retrotransposons, a type of “jumping gene” that inserts into the genome and duplicates.

cont’d

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Jovial Monk

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Re: Where Do Viruses Come From?
Reply #1 - Dec 2^nd, 2025 at 11:54am

Quote:

Did Cell Components Escape to Become Viruses?

Genome reduction isn’t the only way that viruses could have emerged from cells. The “escape hypothesis” suggests that viruses could have emerged from a few cellular components that broke loose. Perhaps the most compelling evidence for this comes from the realm Riboviria, which contains retroviruses like human immunodeficiency virus (HIV). Retroviruses are RNA viruses that produce DNA copies of their genomes that they insert into host DNA. It is possible that these arose from retrotransposons, a type of “jumping gene” that inserts into the genome and duplicates.

In a study published this year, John O’Brien, an evolutionary virologist at the University of Oxford, and his colleagues mathematically modelled how the escape hypothesis could produce viruses. Their model predicts that viruses could have emerged if ancient cells divided unequally, allowing jumping genes or other self-replicating nucleic acids to break away from the genome. They tested out different rates of unequal division.

“What we found is that it does have to be happening commonly in order for viruses to arise via this method,” O’Brien said. “There should be a 50 percent chance every time a cell divides that there is an unequal cell division,” he added. “That is a critical part.” This may explain why most viral realms emerged near the dawn of life, when less robust cells with more fallible cell division dominated, he explained.

Though the escape hypothesis has garnered more support, some biologists believe multiple origin theories could apply to a single realm and have developed the “chimeric origin hypothesis,” which merges the escape and virus-first hypotheses. Bisio is fond of the hybrid theory, which assumes viruses evolved in a modular fashion, starting with replication machinery and then adding on capsid proteins later.

https://www.the-scientist.com/where-do-viruses-come-from-73720

Sources cited in article:

https://www.the-scientist.com/rna-from-the-origin-of-life-to-the-future-of-medic...

https://www.the-scientist.com/giant-viruses-grew-out-of-small-ones-study-70949

https://ictv.global/files/proposals/pending

References:
Men Y, et al. Reconstruction of the rRNA sequences of LUCA, with bioinformatic implication of the local similarities shared by them. Biology. 2022;11(6):837.

Simmonds P, et al. Four principles to establish a universal virus taxonomy. PLoS Biol. 2023;21(2):e3001922.
The International Committee on Taxonomy of Viruses. Reorganization of the realm Monodnaviria by moving three of the four kingdoms to new realms and renaming the realm Monodnaviria to “Floreoviria.” Published online 2025.

Forterre P. The origin of viruses and their possible roles in major evolutionary transitions. Virus Res. 2006;117(1):5-16.

Blank CE. Not so old Archaea – the antiquity of biogeochemical processes in the archaeal domain of life. Geobiol. 2009;7(5):495-514.

Miao L, et al. 1.63-billion-year-old multicellular eukaryotes from the Chuanlinggou Formation in North China. Sci Adv. 2024;10(4):eadk3208.

Mughal F, et al. The origin and evolution of viruses inferred from fold family structure. Arch Virol. 2020;165(10):2177-2191.

Zomorodipour A, Andersson SGE. Obligate intracellular parasites: Rickettsia prowazekii and Chlamydia trachomatis. FEBS Letters. 1999;452(1-2):11-15.

Koonin EV, Yutin N. Multiple evolutionary origins of giant viruses. F1000Res. 2018;7:1840.

Naqvi AAT, et al. Insights into SARS-CoV-2 genome, structure, evolution, pathogenesis and therapies: Structural genomics approach. BBA. 2020;1866(10):165878.

Thomy J, et al. Eukaryotic viruses encode the ribosomal protein eL40. npj Viruses. 2024;2(1):51.

Bisio H, et al. Evolution of giant pandoravirus revealed by CRISPR/Cas9. Nat Commun. 2023;14(1):428.

Goettel W, Messing J. Change of gene structure and function by non-homologous end-joining, homologous recombination, and transposition of DNA. PLoS Genet. 2009;5(6):e1000516.

Wang J, Han GZ. A Missing link between retrotransposons and retroviruses. mBio. 2022;13(2):e00187-22.

O’Brien JT, et al. The origins of viruses: Evolutionary dynamics of the escape hypothesis. Front Virol. 2025;5:1555137.

Sauguet L. The extended “two-barrel” polymerases superfamily: Structure, function and evolution. J Mol Biol. 2019;431(20):4167-4183.

De Farias ST, et al. Origin and evolution of RNA-dependent RNA polymerase. Front Genet. 2017;8:125.

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