Paleovirology: The Study of Endogenous Viral Elements
Amr Aswad and Aris Katzourakis
from: Virus Evolution: Current Research and Future Directions (Edited by: Scott C. Weaver, Mark Denison, Marilyn Roossinck and Marco Vignuzzi). Caister Academic Press, U.K. (2016) Pages: 273-292.
Viruses sometimes heritably integrate into the genomes of their hosts, resulting in genomic features known as endogenous viral elements (EVEs). Using EVEs, the field of paleovirology investigates the long-term evolution of viruses and their impact on hosts. One of the fruitful outcomes of high throughput genomics is the widespread availability of whole genome data, offering the unprecedented opportunity to investigate EVEs at a large scale. In this chapter, we review the consequent surge in paleovirology research that can be traced to landmark work performed over half a century ago. We describe general principles of EVE biology and the main methodological techniques used to study them. We show how EVEs can only be understood within an evolutionary framework and we outline a generalized workflow for conducting paleovirology studies. We review exemplar paleovirological discoveries from each of the main viral groups, highlighting a range of approaches to paleovirology. We also discuss the major implications that certain discoveries and insights from paleovirology could have on our understanding of both virus and genome evolution. Finally, we consider the current limitations and potential pitfalls in paleovirology, and anticipate the possible future directions of this exciting and rapidly growing field read more ...