Posted by RJG on April 15, 2013 • Paleovirology
What is paleovirology?
Paleovirology addresses the long-term evolutionary history of viruses. Traces of this history are embedded in the biodiversity of contemporary species. For example, the architectures of proteins and nucleic acids contain information about the early evolution of viruses [1, 2], and in host species, the sequences of 'antiviral' genes contain the signatures of their epic evolutionary conflicts with viral antagonists [3, 4, 5].
Another means by which the ancient history of viruses can be investigated is through recovery of the viral 'fossil record' [6, 7, 8]. Eukaryotic genomes contain thousands of DNA sequences that are derived from ancient viruses. These endogenous viral elements (EVEs) arise when infection causes genetic material derived from a virus to become integrated into the host germline, such that viral genes can be inherited as host alleles. Over millions of years, repeated genome invasions by viruses have occurred, and some of the resulting EVEs have become fixed in the host germline - these DNA sequences are viral fossils.
Recent years have seen vast advances in the affordability and power of DNA sequencing technologies, and genome sequence data are accumulating at an accelerating pace. This deluge of sequence data provides unprecedented scope for paleovirological studies of the virus fossil record.
A playful black-and-white ruffed lemur.
Investigating viral diversity in Malagasy mammals
The West African microcontinent of Madagascar is often described as 'the world's oldest island'. Paleogeological studies indicate that the landmass formed more than 100 million years ago, and has since remained in its present position, approximately 300 miles West of the Southern African mainland.
The extraordinary mammalian fauna of Madagascar reflect this unique biogeographic history. Paleontological evidence indicates that the island originally had no native mammal species. The indigenous terrestrial mammals are derived from a small number of founder populations that reached Madagascar by 'rafting' or 'island-hopping'. These colonizing populations entered an environment in which many mainland species were absent, launching them along a unique ecological and evolutionary trajectory.
We are currently investigating viral diversity in Malagasy mammals. We aim to recover information about the long-term evolutionary history of viral infections in Malagasy mammals through exploration of the the viral fossil record and characterization of viruses infecting contemporary species.
The epidemic within
env-less ERVs are genomic superspreaders
Endogenous retroviruses (ERVs) are a unique combination of pathogen and selfish genetic element. Some ERV lineages proliferate by infecting germline cells like typical retroviruses, while others behave like retrotransposons, replicating entirely within the host cell. In these retrotransposon-like ERVs, the envelope (env) gene required to infect cells becomes redundant and degrades over time, often being lost entirely.
To examine the factors that determine the relative abundance of different ERV lineages, we analyzed over 5000 ERV loci recovered from 38 mammal genomes. This analysis revealed that ERVs lacking the env gene have undergone massive proliferations in their host genomes, and that where ERVs have adapted to replicate intracellularly, their proliferation within the host germ line is boosted by a factor of ~30. This parallels infectious disease epidemics, where commonly ~20% of the infected individuals are responsible for 80% of onward infection.
Horses in Outer Mongolia.
Geographic structuring of equine infectious anemia virus isolates
Equine infectious anaemia virus (EIAV) is a lentivirus that infects horses worldwide. Uniquely among known lentiviruses, EIAV can be mechanically transmitted by arthropods (particularly horse flies). EIAV infection is often asymptomatic, but can also manifest as an acute, fulminant disease with high-titre viremia. In an collaborative investigation of genetic diversity among globally sampled EIAV isolates we found clear evidence of geographic compartmentalization, with distinct strains being predominant in Asia, Europe and the Americas . In addition, our study found evidence that the majority EIAV strain found in the Americas originated approximately 400 years ago - around the time that horses were reintroduced to the New World by European colonists.
Equids became extinct in the Americas ~12,500 years ago, and were not re-introduced until the late 15th Century . Prior to the development of reliable serologic tests in the early 1970s, it was virtually impossible to distinguish inapparent carriers of EIAV from uninfected animals , and European colonists likely introduced the disease to the Americas unwittingly.