Two viruses that no one had ever described have just been identified in tissues from short-finned pilot whales and killer whales

Two viruses that no one had ever described have just been identified in tissues from Caribbean short-finned pilot whales and killer whales. The study, published on 6 January 2026 in Virology, does not say that they make the animals carrying them ill. It says that they exist, that they were invisible, and that what they do is unknown. That is precisely what makes it interesting.

What a circovirus is

Circoviruses are among the smallest viruses known to infect animals: a circular single-stranded DNA genome of about two thousand bases, a protein shell, and nothing else. No envelope, very few genes, complete dependence on the host cell’s machinery.

This simplicity says nothing about how harmless they may be. Porcine circovirus type 2 is responsible for a wasting disease that has cost European pig farming dearly, and its main mechanism is immunosuppression: the virus does not attack directly, it weakens the defences and lets the rest follow. In cetaceans, a circovirus described earlier in a beaked whale had already been suspected of an effect of this kind.

Where the samples come from

The material was not collected for this study. It comes from archived tissues of dead animals, obtained through a collaboration with the artisanal subsistence hunters of Saint Vincent, in the Lesser Antilles, where a traditional pilot whale hunt survives under regulation.

This point is worth noting for its own sake. A good part of what is known about the health of the large cetaceans comes from material that was not chosen: strandings, bycatch, regulated hunts. Live animals offshore do not lend themselves to routine biopsy, and the tissue collections built up over the decades now serve questions that nobody was asking when they were assembled.

Seven complete genomes

The team, gathered around Arvind Varsani at Arizona State University with Matthew De Koch as first author, put these tissues through high-throughput sequencing. This approach does not look for one virus in particular: it reads everything present in the sample, then sorts.

Seven complete circovirus genomes came out of it: five in short-finned pilot whales, two in killer whales. Different enough from the known circoviruses to constitute two new species, which the authors have named shofin circovirus and orcin circovirus. This is the first detection of cetacean circoviruses in this region of the North Atlantic.

The collaboration extends beyond North America: Coastal Carolina University, the University of the South, the University of the West Indies at Cave Hill in Barbados, the University of Cape Town in South Africa and the Institut Pasteur are among the signatories.

A structural peculiarity

The two viruses share an unusual trait: their capsid protein carries surface-exposed loops that are abnormally long. The loop known as E-F is close to twice the length of the one in porcine circovirus type 2.

These loops are the part of the virus that the immune system meets first, and the part that determines what it attaches to. So different a geometry suggests either a different type of target cell or a different way of escaping antibodies. Suggests only: no experiment has been carried out on this point.

An origin that may be very ancient

The position of these two viruses in the circovirus tree leads the authors to a hypothesis they frame with caution: circoviruses could have infected the ancestors of modern cetaceans early in their evolutionary history, that is, at the time when these animals were returning to the water.

The hypothesis is attractive and calls for a great deal more material. Viral genomes from a far wider range of cetacean species would be needed, and preferably from both of the major groups, to check that the resemblance between viruses follows the relatedness between hosts. The authors say so themselves: the demonstration remains to be made.

Three questions left open

1. Nothing on disease. Finding a virus in a tissue does not prove that it made the animal ill, nor even that it was replicating. Many viruses circulate with no perceptible effect. Establishing a cause-and-effect link would mean comparing affected and unaffected animals, with lesions described, which has not been done.

2. Nothing on transmission. It is not known how these viruses pass from one animal to another, or whether they circulate within the very tight social groups that pilot whales and killer whales form. The question is not trivial: an immunosuppressive pathogen in a small and socially dense population behaves differently from one in a dispersed population.

3. A tiny, localised sample. Seven genomes, two host species, one region. The true prevalence is unknown, and nothing says that these viruses are confined to the Caribbean. The short-finned pilot whale is in fact found in French overseas waters, where it is regular in the Antilles as in New Caledonia.

The exercise still has a value of its own. Searching without a hypothesis in material already collected reveals a layer of marine life that nobody was looking at, and raises questions that one did not know had to be asked.

Source: De Koch M., Varsani A. et al., “Novel circoviruses identified in short-finned pilot whale and orca from the North Atlantic Ocean”, Virology, volume 615, article 110768, 6 January 2026.