Retroviruses (Retroviridae) — a family of viruses that includes pathogens such as HIV, feline leukemia, and several cancer-causing viruses — have an ancient marine origin and originated together with, if not before, their jawed vertebrate hosts nearly 450 million years ago in the Ordovician period, according to a new study published today in the journal Nature Communications.
Retroviruses are a group of medically and economically important viruses.
The ‘retro’ part of their name comes from the fact they are made of RNA, which they can convert into DNA and insert into their host genome – the opposite direction to the normal flow of information in a cell.
This property means that they can occasionally leave genomic fossils within their host genome, known as endogenous retroviruses.
Retroviruses are broadly distributed among vertebrates and can also transmit between hosts, leading to novel diseases such as HIV, and they have been shown to be capable of leaping between distantly related hosts such as birds and mammals.
But until now, it was thought that retroviruses were relative newcomers – possibly as recent as 100 million years in age.
“Our new research shows that retroviruses are at least 450 million years old, if not older, and that they must have originated together with, if not before, their vertebrate hosts in the early Paleozoic era,” said Dr. Aris Katzourakis, an evolutionary biologist and paleovirologist in the Department of Zoology at the University of Oxford, UK, and corresponding author on the study.
“Furthermore, retroviruses would have been present in our vertebrate ancestors prior to the colonization of land and have accompanied their hosts throughout this transition from sea to land, all the way up until the present day.”
Dr. Katzourakis and his Ph.D. student, Pakorn Aiewsakun, used genome sequences from endogenous retroviruses that resemble the ‘foamy’ viruses, a group of viruses that tend to diverge alongside their hosts.
“Foamy viruses are a unique subgroup of retroviruses (genus Spumaretrovirus) that are characterized by an extremely stable history of co-speciation with their mammalian hosts, at least since the origin of eutherians about 100 million years ago,” the researchers said.
“This unique evolutionary feature, together with the high availability of foamy virus molecular data, allows their evolutionary dynamics to be described in unprecedented detail, making foamy viruses one of the most important models of retroviral macroevolution.”
Foamy viruses are widespread in mammals, and in this study the authors identified genomic fossils for foamy-like retroviruses in highly diverse hosts, including ray-finned fish and amphibians in which they had not previously been found.
“We report 36 lineages of basal amphibian and fish foamy-like endogenous retroviruses (FLERVs),” the scientists said.
“Phylogenetic analyses reveal that ray-finned fish FLERVs exhibit an overall co-speciation pattern with their hosts, while amphibian FLERVs might not.”
“We also observe several possible ancient viral cross-class transmissions, involving lobe-finned fish, shark and frog FLERVs.”
During the study, the team overcame one of the key limitations in studying the deep evolutionary history of viruses: their rapid evolution. This trait facilitates the reconstruction of viruses’ recent history but obscures their more distant past.
However, a new model used by the authors – in combination with the genomic fossil records of the foamy-like viruses – allowed them to account for an apparent slowdown in the rate of evolution the further back they went.
“These findings show that this medically important group of viruses is at least up to half a billion years in age – far older than previously thought,” Dr. Katzourakis said.
“They date back to the origins of vertebrates, and this gives us the context in which we should consider their present-day activity and interactions with their hosts.”
“Our inferred date of the origins of retroviruses coincides with the origins of adaptive immunity, and thus it is likely that retroviruses have played an important role in the emergence of this key tool in vertebrate antiviral defense,” Dr. Katzourakis added.
“As we understand the nature of the interaction between viruses and host immunity, we will be better placed to intervene in this delicately balanced arms race in order to develop novel treatments and interventions.”
“And as we build a clearer picture of the origins of the diverse groups of viruses that infect us today, we should come closer to unraveling the mystery of their ultimate origins.”