Snake viruses have a lot to tell

Snakes have inhabited the Earth for more than a hundred million years. Viruses present in snakes can reveal surprising and interesting things about viral evolution and their mechanisms of action.

When Jussi Hepojoki started working at the University of Helsinki after graduating with a bachelor’s degree in biotechnology, he had no intention of becoming a researcher. However, the fascination of viruses turned out to be irresistible.

“So, I completed a master’s degree in biochemistry and defended my doctoral dissertation on virology in 2011.”

Today, Hepojoki works as an Academy of Finland research fellow at the University of Helsinki and a senior lecturer at the Vetsuisse Faculty of the University of Zurich, studying – perhaps somewhat surprisingly – snake viruses.

Hepojoki’s interest in snakes was the result of a coincidence. In 2012 Udo Hetzel, then working as a docent at the Faculty of Veterinary Medicine, University of Helsinki, paid a visit to a weekly seminar held on Meilahti Campus for virologists specialised in zoonotic viruses. Hetzel is a veterinary pathologist specialised in exotic animals, such as constrictor snakes, with a particular focus in a field known as ultrastructural pathology, in which changes in the fine structure of tissues are investigated. The visit engendered close cooperation between Hetzel and zoonotic virology specialists at the University of Helsinki.

In 2013 Hetzel moved to the Vetsuisse Faculty of the University of Zurich. As another result of the collaboration, Hepojoki joined him to spend a year in Zurich in 2016.

“At first, we had a few snakes here in Helsinki, too. Once the colleagues who had worked with them relocated to Switzerland, the snakes became my responsibility. They were only snakelets, and I had to teach them to eat – there were a few complications, but eventually they learned and started growing very well,” Hepojoki reminisces.

“These days we primarily study snakes that are examined at the Institute of Veterinary Pathology in Zurich, in close collaboration with snake breeders, while in Helsinki we focus on their viruses.”

So far, viruses have been extracted only from snakes in human care, which leaves researchers uncertain about whether the viruses identified also occur in snakes living in the wild. The current project involves looking for viruses in snakes living in nature in Africa, South America and, in the future, regions of Asia.

A virus named after the University of Helsinki and the Haartman Institute

In 2012 Hepojoki and Hetzel initiated “The BIBD Group” and started investigating a chronic infectious disease found in boas and pythons (boid inclusion body disease, BIBD), known since the 1970s, with the cause remaining unknown. The research resulted in the identification of a new arenavirus species. The discovery was published in October 2013 in the Journal of Virology, and ended up as the cover story.

“Earlier it was thought that representatives of the family Arenaviridae only occurred in rodents and bats, but then they were also found in snakes. A little before us an American group of researchers reported similar viruses, which they named after a research institute and the Golden Gate Bridge. Therefore, we ended up naming the virus we found as University of Helsinki virus-1,” Hepojoki explains.

The viruses identified in the snakes differed from previously known arenaviruses to such a degree that the family Arenaviridae was divided into two genera, Reptarenavirus and Mammarenavirus.

“Soon after that, we found an arenavirus in snakes that was so different from earlier viruses that it could not be classified under the genus Reptarenavirus. This new virus species was named Haartman Institute snake virus-1 (HISV-1). More similar viruses were found later, thus giving rise to genus Hartmanivirus.”

Snake cells infected by reptarenaviruses begin to accumulate protein plaques called inclusion bodies. In pythons, the disease often causes neurological symptoms, though this is less common in boa constrictors. In boas at least, a reptarenavirus infection is permanent, so while the disease may progress very slowly, it will most likely eventually be fatal.

Hartmaniviruses are often found in snakes infected by reptarenaviruses, but so far the role of the former in the pathogenesis of BIBD is unknown.

“Apparently snakes start developing other secondary infections and malignant tumours, which eventually kill them. As yet, we remain uncertain about the mechanisms of the disease, but we suspect that the reptarenavirus weakens the snake’s immune defences, resulting in an outcome similar to that of an untreated HIV infection in humans,” Hepojoki says.

“Research on arenaviruses found in snakes helps understand the mechanisms viruses employ to maintain persistent infections.”

RNA viruses are masters of adaptation

Hepojoki finds RNA viruses, to which arenaviruses also belong, particularly interesting and also extremely frightening due to the fact that they are exceptionally good at adapting. This feature makes many of them able to transfer from one species to another. Certain rodent arenaviruses have the ability to infect humans in whom they can cause very serious diseases, including Lassa fever.

The arenaviruses thus far identified in snakes are not known to cause diseases in humans.

“In fact, they are able to infect all types of cells, and in laboratory conditions they can also grow in human cells, but only at the temperature of 30 degrees Celsius. At normal body temperature, their growth slows down or is entirely inhibited.”

The ability of viruses to cross species barriers is a matter of great interest to researchers. What happens to the genome of a virus that transfers into a new species and how does it adapt its functions to the immune system of the new host?

Viruses manipulate the immune defences of their host species by pressing either ‘brake’ or ‘gas pedal’. In a new host, this braking and accelerating by the virus may, however, cause an entirely new kind of defensive reaction, something that may even kill the host – naturally an unwanted outcome for the virus.

“For viruses to keep on growing in a new host, they have to learn to cope with new kinds of defences. How does this adaptation happen in practice? That’s an interesting question.”

What is a mystical deltavirus doing in a snake?

Only recently, the same group of researchers from the Universities of Helsinki and Zurich published another unexpected finding: they had identified a deltavirus carried by a snake (MBio, 2 April 2019). Until then deltaviruses were thought to only occur in humans, and only in co-infection with the hepatitis B virus.

“Deltaviruses are viruses of a very special kind. They only have one single string of proteins, comprising roughly one-third of the virus. The rest is what is known as ‘garbage RNA’, due to which it is easy to miss the virus in sequencing,” Hepojoki says.

On their own, deltaviruses are incapable of infecting cells; rather, they need a viral companion whose surface structures they exploit. In humans, deltaviruses are only able to cause an infection either together with the hepatitis B virus or by infecting humans already suffering from hepatitis B.

“Identifying the virus in a snake raises the question of whether it is, after all, able to employ helper viruses other than hepatitis B. As this would be a rather significant discovery, we are keen to demonstrate this in practice. For the time being, researchers have not identified anything similar to the hepatitis B virus in snakes carrying deltaviruses, which indicates that the latter may well be also using other viruses for transport.”

Incredibly limited knowledge of viruses

We have identified only an infinitesimally small number of all the viruses in the world, perhaps only one-hundredth of one per cent. According to Jussi Hepojoki, an Academy of Finland research fellow, we know incredibly little about them.

“When you consider viruses and us humans, we are really such a small species here on Earth. Our entire history is just a blink of an eye on the scale of the Earth’s history – and it seems that our time here may not extend that much further.”

Knowledge gained from viral research may be among the factors providing humanity a little additional time here on Earth.

Now, thanks to novel sequencing techniques, new viral species, genera and families are being continuously identified. However, what is even more interesting than finding new species is looking into how different viruses function, what kinds of mechanisms they use in infecting their hosts, how they manipulate the immune system of their host, and how they cross species barriers and adapt to new conditions.

Knowledge gained from viral research may be among the factors providing humanity a little additional time here on Earth. Without sufficient knowledge of the workings and effects of viruses, humanity may not necessarily survive attacks by constantly evolving viruses. Dangerous pandemics on the global scale remain possible – even likely.

Genuine innovations are nothing if not ‘by-products’ of basic research.

“This research on snake viruses is basic research which produces information that can be used to conduct applied research, such as developing new antiviral medication."

Hepojoki admits that he is not chiefly interested in applied research, even though he has, among other activities, contributed to the development of important point-of-care diagnostics.

“I want to work in a laboratory, to carry out research and make discoveries, to come up with solutions without having to consider how to turn the findings into practical applications and marketable products as quickly as possible. Without this kind of basic research, we will soon have nothing to apply and market, since genuine innovations and significant discoveries are nothing if not ‘by-products’ of basic research.”