Fossils are a key resource for understanding the evolutionary history of species – but for viruses, this source is not available in the same way as traditional fossils.
In a new study, researchers examined a wide variety of vertebrates (animals with backbones) for endogenous viral elements (EVEs) – virus sequences integrated into other species’ genomes. They discovered four virus families that had not been found in vertebrates previously, adding to the nine previously known. Through their analysis, they found the first virus sequences of a hepacivirus (Hepatitis C-like virus) and a nairovirus (related to Crimean Congo Haemorrhagic Fever virus) in the genomes of mice and rats (murine rodents), and the Etruscan shrew respectively, highlighting the close connection of these animals with potentially pathogenic viruses. Dr Jose Gabriel Nino Barreat said:
“We were surprised to discover such diverse viral fossils in the genomes of vertebrates, including EVEs from less well-known viral families; this indicates that the diversity of ancient virus fossils in animal genomes is larger than previously thought, enabling the deep evolutionary history and paleoecology of more viral families to be studied in greater detail.”
Over millions of years, viral sequences have accumulated in the DNA of animals, leaving a rich fossil record of ancient viruses and their interactions. Their discovery can help us better understand which hosts the virus infects and where in the world the virus has been – and additionally establishes a direct timeline of association between the virus and its host. Professor Aris Katzourakis said:
"Understanding the time scale of association between these highly pathogenic viruses and their hosts could pave the way to novel avenues to prevent and treat viral disease."
The study took advantage of the increasing amount of sequence data available together with cloud technologies to allow a comprehensive analysis, and highlights the role that this technology can play in viral surveillance and understanding the true diversity of viruses.
The researchers also discovered evidence of benyviruses, which are known to infect plants, infecting diverse species of animals, from great white sharks to legless amphibians called caecilians. This expands our knowledge of the ecology of benyviruses by suggesting some may infect a wide diversity of animal hosts. Professor Aris Katzourakis said:
"The discovery of otherwise animal infecting viruses in plants indicated that we may need to survey plants more extensively to understand the origins of animal viruses as well"
The analysis also revealed that a region of the envelope protein (called ectodomain) of filoviruses (like Ebola virus) and reptile-infecting arenaviruses likely evolved in retroviruses first, and was then captured by filoviruses and reptarenaviruses three different times during evolution. This suggests that there is an important evolutionary advantage obtained by acquiring the ectodomain, likely related to its function in suppressing the host’s immune system.
The research reveals key insights into the evolutionary interactions between several potentially pathogenic viruses (e.g. relatives of viruses which cause haemorrhagic fevers and hepatitis) and their hosts, which could shed light on their origins and infectious disease ecology.
To read more about this research, published in Nature Microbiology, visit: https://www.nature.com/articles/s41564-024-01825-4
