In the rivers of New Jersey, a story was unfolding in the bodies of alewives, a species of river herring that has long been a vital part of North America’s aquatic ecosystems. These silvery fish, known for their springtime spawning runs, became the focus of a fascinating scientific discovery made by Raines and colleagues.

This study was motivated by a broad mission to uncover potential threats to fish health in local waterways. What they found was both surprising and groundbreaking, a previously unknown virus quietly circulating in fish that appeared to be otherwise healthy.

This virus belongs to the Hepadnaviridae family, a group best known for containing the human hepatitis B virus. However, the newly discovered virus, dubbed alewife hepatitis B virus (ApHBV), is likely not something that affects people. Instead, it seems to be a fish-specific virus that had never been documented.

Using cutting-edge genetic tools, the researchers analysed tissues from hundreds of alewives collected between 2015 and 2018. While none of the fish showed any outward signs of illness, the team’s sensitive testing methods revealed viral genetic material in several of them, particularly in adult fish returning to freshwater rivers to spawn.

One of the remarkable aspects of this discovery is that the infected fish appeared completely healthy. There were no signs of disease, no tissue damage under the microscope, and no immediately obvious indication of stress or weakness. This raised interesting questions: Could the virus be harmless? Or might it become dangerous under the right (or wrong) circumstances?

Raines and colleagues didn’t stop at detection, they sequenced the entire genome of the virus and compared it to other known viruses. Their analysis showed that ApHBV is most closely related to a group of fish viruses known as metahepadnaviruses, which have only recently begun to be understood by scientists.

The implications of this discovery are broader than they may seem. River herring like alewives have been in decline for centuries due to factors including overfishing, damming of rivers, pollution, and habitat degradation. Federal researchers, including NOAA Fisheries, report that river herring populations have declined by as much as 98% since the 1700s.

As these fish populations struggle to recover, understanding any possible health threats, whether now or in the future, is crucial to conservation efforts. Happily, for now, there’s no evidence that this virus is harming the alewife population and it is essentially an invisible passenger in affected fish. Regardless of whether new viruses discovered by researchers pose a direct threat to humans or wildlife at the point of discovery, it’s important to keep looking for anything that helps us expand our understanding of existing viruses and the conditions under which they could post a threat. Collecting this type of knowledge helps us figure out what we have still yet to learn and may provide clues against new threats that could emerge in the future.

Unlike the invisible alewife virus, another virus discovered by Raines and collaborators in bass makes its presence known. If you’ve ever gone fishing and pulled up a bass with strange dark blotches across its skin, you’re not alone, and you’re not seeing things. Anglers and biologists across the United States have noticed an increasing number of smallmouth and largemouth bass sporting unusual black patches, a condition now known colloquially as “Blotchy Bass Syndrome” (or BBS) by anglers. But what exactly causes these dramatic skin changes in this iconic sportfish?

This work, originally led by Dr. Luke Iwanowicz during his tenure as a USGS research biologist and continued by Dr. Clay Raines at USGS, has finally connected the dots after decades of speculation. Their work has uncovered a microscopic culprit behind the mystery: newly discovered members of an emerging group of viruses called adomaviruses, which are still poorly understood.

Black bass are more than just popular sportfish, they’re central to a multibillion-dollar angling industry and are ecological cornerstones in freshwater habitats. So, when these fish started showing blotchy, black lesions, it sparked concern among anglers, fisheries managers, and scientists alike.

These strange marks weren’t just a few odd cases, observations have been made nationwide. In some areas, like Lake St. Clair in Michigan, surveys showed that over 5% of bass exhibited these symptoms annually since 2008. In Virginia tributaries of the Potomac River, up to 23% of largemouth bass were affected. The blotches were primarily seen during the spring and mainly in adult fish. Yet for years, the cause remained elusive.

In an impressive scientific sleuthing effort, Clayton Raines and the rest of the blotchy bass team investigated skin samples from affected fish across the country. In one study, using advanced genetic tools, they identified not just one, but two novel viruses associated with these lesions, one in smallmouth bass and another in largemouth bass.

The two viruses, while related, were unique to their host species. This suggests the viruses evolved alongside their respective bass hosts over thousands, possibly millions, of years. What’s especially fascinating is how the team demonstrated a strong link between the viruses and the skin symptoms. Viral material was consistently found in the blotchy lesions and was largely absent in healthy skin.

The researchers also discovered that the dark blotches are likely part of the fish’s own immune response. The virus seems to infect skin cells first, and the host’s defense mechanisms, possibly involving cells called melanocytes, respond by migrating to the site of viral infection, creating the telltale spots.

The timing of the disease also lines up with seasonal changes in the fish’s biology. The blotches are most prominent in spring, a time when fish are preparing to spawn and hormone levels rise. These internal changes might affect how fish respond to the virus.

In a more recent study, Raines and colleagues discovered an entirely new group of viruses living within a single skin lesion of a largemouth bass. Not one, not two, but four distinct viruses were found in just one fish sampled from Little Hunting Creek, a tributary of the Potomac River in Virginia. Strikingly, three of the viruses had not been previously discovered.

Until now, only a handful of viruses were known to infect largemouth bass, and only two are typically considered in cases of fish die-offs. But Raines’ research changes that picture dramatically, suggesting that a much more complex and understudied viral ecosystem may be impacting fish health, and potentially the sportfishing industry as a whole.

Among the newly discovered viruses was a nackednavirus, a distant viral relative of hepatitis B viruses found in humans. This was the first time such a virus was documented in largemouth bass. The team also found three adomaviruses.

The big question remains: is blotchy bass syndrome harmful? So far, there’s no clear evidence that it causes widespread health issues or kills fish. In fact, bass have been observed with these spots for decades, especially largemouth bass, without apparent long-term impacts. However, the presence of a virus means fish health could still be affected under stressful conditions, such as high-water temperatures or poor water quality. This underscores the importance of advanced genetic screening techniques like next-generation sequencing. Traditional diagnostic methods would likely have missed these silent infections.

This research adds to the growing awareness of how much we still don’t know about the viral world in aquatic ecosystems. Fish, like humans and other animals, host a wide variety of viruses, many of which may never cause illness but could still play important roles in evolution, ecology, or disease under the right conditions.

But as temperature instability, habitat loss, and other pressures continue to mount, ongoing surveillance will be key. Thanks to researchers like Clayton Raines and his colleagues, we’re beginning to peer beneath the surface, to better understand the delicate balance of life in our rivers and seas.

This research opens the door to better monitoring and informing management, especially in fisheries and aquaculture settings. It also serves as a reminder of the inherent complexity of nature. What looks like a simple skin blotch can, reveal clues about viral evolution, immune defence, and environmental change.

The study also raises red flags about potential risk factors where viruses may spread, through stocking programs, fish handling, or even boats traveling between water bodies. And as global temperatures rise, fish may become more vulnerable to stress and infections, increasing the risk of outbreaks.

While none of the newly discovered viruses have been directly linked to serious disease (yet), their presence, especially in combination, suggests that fish may be more vulnerable than previously thought. It’s a wake-up call for fishery managers, aquaculture facilities, and researchers alike. Thanks to scientists like those at USGS Eastern Ecological Science Center, the pieces of this puzzle are finally coming together, helping us better understand and protect the species that populate our lakes, rivers, and live wells.