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Science Not yet confirmed elsewhere1 publisher 2 min read Published

Newly found small-genome viruses suggest encapsulins and viruses evolved from each other repeatedly

University of Miami researchers identified previously unknown viruses that bridge viruses and encapsulin compartments in cells, Phys.org reported. The Nature Communications paper reports evidence that the two lineages evolved from one another repeatedly over millions of years. That contests the theory that encapsulins simply descended from viruses.

The Scientist · Science desk

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What happened

  • HK97-fold proteins assemble into protein shells, and that shell structure turns up in both viruses and encapsulins.
  • The new viruses have genomes smaller and simpler than other HK97-fold shell formers, and they share features with both viruses and encapsulins.
  • The team applied bioinformatics, biophysical models, protein language models and AlphaFold to structural information from databases of billions of DNA sequences.
  • Those sequences came from soil, seawater, wastewater, the human gut and other sites worldwide, including the IMG/M database.

Why it matters

  • What doesn't add up contradiction The missing-link label suggests a single bridge between two groups, but the paper's claim is repeated exchange over millions of years. That would take many crossings.
  • What's now possible capability The paper names a route through procapsids, so the repeated-exchange idea can be checked against particular immature shells.
  • What it limits constraint This is one Phys.org report of one Nature Communications paper. It does not show how strong the evidence for repeated exchange is.

First author Abelardo Aguilar, a doctoral student in biology at the University of Miami, in its College of Arts and Sciences, ties the shared fold to a larger question [12]. "These proteins build compartments with two different roles, which connects directly with the study of the origin of life and its early evolution because if you think about it, life at its core is about enclosing reactions and also enclosing information that can be inherited so those reactions can happen in the future," he said [11].

That framing explains why the claim is about direction. A virus with features of both groups shows the groups are connected [8]. Whether it sits on a path from viruses to encapsulins, the reverse, or both is an inference from sequence and structure, and the authors read it as running both ways, repeatedly [6]. We'd expect a group of intermediates to test the one-way account better than a single find would, because a group lets the pattern recur or fail to.

Sequencing is what made the search possible. "The majority of viruses cannot be grown in the lab. But now through sequencing, we have access to information on viruses for which we don't know the host, that we can't culture in the lab, but that are everywhere," said Antoni Luque Santolaria, the senior author [3][12]. The databases held billions of DNA sequences [1]. The report does not say how many new viruses the search found or whether any has a known host.

Phys.org says the discovery has implications for biotechnology as well as for understanding the origins of life [4]. Aguilar pointed to one possibility on the shell side. "One implication of this research is the possibility that viral capsids could also facilitate biochemical reactions, which would open up the potential roles that capsids have in environments as a whole," he said [10].

What to watch

  • Whether other groups searching sequence databases find further small-genome HK97-fold viruses that show the same two-way pattern.
  • Whether any of the new viruses is tied to a host or grown in a lab.
  • Whether experiments show viral capsids carrying out biochemical reactions, as Aguilar says is possible.

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Evidence55
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  1. [1]

    The team used bioinformatics tools, biophysical models and AI-based tools, including protein language models and AlphaFold, to mine structural information from databases containing billions of DNA sequences.

  2. [2]

    The sequences, in databases that included IMG/M, came from samples of soil, seawater, wastewater, the human gut and other environments collected around the world.

  3. [3]

    "The majority of viruses cannot be grown in the lab. But now through sequencing, we have access to information on viruses for which we don't know the host, that we can't culture in the lab, but that are everywhere," Luque said.

    Reported Supported Source: Antoni Luque Santolaria, via Phys.org2 sources— create a free account to open themView cited source

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Sources

1 independent publisher whose own reporting we read for this story.

  1. phys.org

    1 article · October 15, 2026

    Newly discovered viruses reveal an evolutionary missing link

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