New mega RNA virus may hold the key to mass oyster die-offs

Scientists have discovered a previously unknown virus in farmed Pacific oysters during a mass die-off in B.C., Canada.

The discovery serves as a reminder that growers should exercise caution when moving young oysters internationally and domestically, to prevent potential spread of pathogens, according to a paper published today in the Proceedings of the National Academy of Sciences.

“We’ve recently seen annual mass die-offs in B.C. and elsewhere of Pacific oysters, the most widely farmed shellfish worldwide,” said first author Dr. Kevin Zhong, research associate in the UBC department of earth, ocean and atmospheric sciences (EOAS). “Often, we don’t know the cause.”

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Pacific oysters are the primary shellfish species grown in B.C. with an estimated value of  $16 million in 2023. While mass die-offs have been attributed to various factors including viruses, bacteria, and warming water temperatures, in many cases, there’s no definitive cause.

Mass die-off

The researchers collected 33 oysters from two farms in B.C. during a mass die-off in 2020, as well as 26 wild oysters from 10 nearby sites. RNA analysis revealed the presence of a previously unknown virus, Pacific Oyster Nidovirus 1 (PONV1), in 20 of the dead and dying farmed oysters – but not in healthy wild oysters, suggesting a link between the virus and mortality.

“This discovery highlights how little we know about viruses infecting invertebrates in general and oysters in particular,” said senior author Dr. Curtis Suttle, EOAS professor. “It’s important to investigate mass die-offs in oysters to determine what causes disease. Similar to humans, disease and death is not caused by a single factor, but prevention is not possible until the causes are known.”

Clues from genomes

The virus has one of the largest RNA genomes on record and is only the second nidovirus found in bivalves. Nidoviruses are found in a wide range of animals, including humans; for example, SARS-CoV-2, a nidovirus, causes COVID-19.

“The extraordinarily large genome of this virus makes it particularly fascinating as it pushes the known boundaries of how big RNA virus genomes can get,” said Dr. Zhong. “A larger genome may allow the virus to encode more genes or protein domains, potentially expanding or enhancing its ability to interact with hosts. This discovery offers a rare window into the possible evolutionary mechanisms that enable genome expansion in RNA viruses.”

Global genetic databases revealed 15 closely related viruses in Pacific oysters in Europe and Asia, suggesting they are globally widespread. However, these cases showed no associated mortality.

The viruses are so different genetically from other nidoviruses that the research team has proposed a new family: Megarnaviridae, or ‘large RNA viruses’. PONV1, which the team is proposing to name Megarnavirus gigas, or ‘large RNA virus giant’, and its relatives appear to be specific to oysters, so humans are not at risk from contracting the virus, said Dr. Suttle.

Care when shipping spat

B.C. oyster farmers, like growers elsewhere, often import oyster seed and juvenile oysters, or spat, from domestic and international hatcheries.

“The discovery of the virus is a reminder that growers should use an abundance of caution when moving oyster spat internationally and nationally, as we still know very little about what causes disease in oysters,” said Dr. Suttle. “New pathogens may be introduced when spat are imported. Ultimately, developing rapid tests for detecting potential pathogens is essential for safely importing oyster seed, and identifying the causes of disease and mortality.”

The scientists emphasize the need for further research to understand the link between the virus and mortality in Pacific oysters and stress the need for ongoing monitoring of oyster populations. “This research is not a cause for alarm,” said Dr. Suttle. “Rather,  this is a meaningful step forward in advancing our understanding of oyster health and supporting the long-term sustainability of shellfish aquaculture.”