An unassuming green alga that has lived quietly in laboratory flasks for decades just revealed it carries a giant virus so large, and so stealthy, that nobody had noticed it before.
The find rewrites what scientists thought they knew about how big a virus can grow while still hiding inside a single-celled host.
The work, led by Maria Paula Erazo-Garcia and Frank Aylward of Virginia Tech, shows that the virus, dubbed punuivirus, slips into the alga’s DNA, goes to sleep, then wakes up later to build full virus particles without killing most of its hosts.
Why giant punuivirus matters
Viruses that integrate and then lie low are common in bacteria, animals, and even humans, but only a handful have been spotted in algae.
The new study confirms that latent infection strategies also exist in the oversized world of giant viruses, whose genomes dwarf those of many bacteria.
These huge pathogens fascinate virologists because they blur the line between virus and cell. Finding one that can go dormant suggests algae, which form the base of many food webs, may quietly shuttle viral genes around ecosystems.
Latent giants also interest evolutionary biologists. Because they cut themselves into host chromosomes, they sprinkle new genes across lineages and may spark sudden leaps in innovation.
Finally, a virus that waits instead of killing offers hints about how viruses manage long-term coexistence, an issue that matters when scientists engineer viral vectors for vaccines and gene therapies.
Finding and studying punuivirus
“We could definitely see that there was a virus inserted there,” said Erazo-Garcia. She first saw unusual DNA fragments while screening cultures of Chlamydomonas reinhardtii, a staple of photosynthesis research.
Long-read sequencing confirmed that a 617,000-base-pair viral genome sat inside chromosome 15.
Electron-microscopy snapshots later caught complete virions roughly 200 nanometers wide budding from a small fraction of cells, even though the cultures looked perfectly healthy.
Because only a few cells ignite the viral program at a time, the infection flies under the radar. The team measured two spikes of viral particles, one early and one late in the week-long growth cycle, showing that timing matters for reactivation.
Parallel tests in Swedish lakes and Dutch coastal waters turned up similar viral DNA in wild relatives, hinting that punuivirus-style infections are not a laboratory quirk but part of nature’s routine.
Sizing up the genetic payload
At 617 kilobases, the giant punuivirus ranks among the largest double-stranded-DNA viruses known.
Its genome encodes an integrase, an enzyme that pastes viral DNA into host chromosomes, and several Fanzor nucleases, mobile genes that can cut DNA using RNA guides, a trick reminiscent of CRISPR systems.
Those nucleases, plus hundreds of other genes, are sandwiched between long terminal repeats and flanked by a six-base target-site duplication, molecular fingerprints that helped researchers pinpoint the insertion site.
The virus also carries hallmarks of self-sufficiency: DNA polymerase, major capsid proteins, and its own transcription machinery.
Such complexity suggests punuivirus can fend for itself once it wakes up, relying on the host mainly for raw materials.
The genome lacks obvious “suicide genes” that would lyse the cell, explaining why infected cultures keep growing. Instead, the virus appears content to release modest numbers of particles while most algae remain alive.
Gene editing promise of punuivirus
Because punuivirus slips its DNA neatly into a host chromosome and later excises full-length genomes, biotechnologists see a potential delivery tool.
The built-in integrase and Fanzor nucleases might help shuttle large cargos into plant or algal genomes more cleanly than current viral vectors.
“It was not known that this could happen in viruses that are quite so big as this one,” said Aylward, noting that the alga stays healthy even while the virus inserts and removes giant stretches of DNA.
Fanzor nucleases are guided by short RNA molecules, much like CRISPR-Cas enzymes, but they cut DNA in a different way.
Harnessing them could broaden the menu of gene-editing tools, especially for organisms where CRISPR struggles.
Researchers also want to dissect the molecular alarm clock that flips punuivirus from silent to active. Understanding that trigger could let engineers program on-demand expression of therapeutic genes without permanent activation.
Gene editing, giant viruses, and the future
The team plans to map every transcript and protein made during the virus’s two production bursts to learn which genes turn the switch.
They also hope to test whether environmental cues, light, nutrients, or stress, nudge the virus awake.
Ecologists, meanwhile, will survey lakes and oceans for other dormant giants. If latent viruses prove common, their slow-motion gene traffic could reshape how scientists think about microbial evolution and carbon cycling.
The discovery shows that even in 2025, familiar lab organisms can hide astonishing secrets, waiting for a curious grad student and a new sequencing machine to bring them to light.
The study is published in Science.
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