Paleovirologia: inferir a evolução viral a partir dos dados da sequência do genoma do hospedeiro

quinta-feira, março 16, 2017

Paleovirology: inferring viral evolution from host genome sequence data

Aris Katzourakis

Published 12 August 2013.DOI: 10.1098/rstb.2012.0493

Source/Fonte: Bioinformatics ***** Site

1. Introduction

Paleovirology is the study of ancient viruses, typically over prehistoric or geological timescales. There is no physical ‘fossil record’ of viruses; virions persist for short time periods, and rapidly degrade leaving no direct trace of their existence. Many viruses can enter the genomes of their hosts—some, such as retroviruses, do so as an obligate step during their replication process, and others can occasionally do so, either by accident or as a latent part of their life cycle. When viral integrations occur in the germline of their host, they can be passed on to the next generation, potentially fixing in the host population. When this occurs, the integrated endogenous virus genomes evolve at host rates of mutation, and their sequence is relatively stably preserved. The study of this genomic ‘fossil record’ has led to the burgeoning field of paleovirology, which uses these endogenous viruses to disentangle the long-term evolutionary history of virus–host interactions.

Viruses are a pervasive feature of both eukaryotic and prokaryotic life, and offer some of the best-studied examples of evolution in action due to their rapid rates of evolution. We have observed the diversification of HIV into distinct subtypes over the past six decades, variously prevalent in different patient risk groups and geographical locations, as well as the selection of drug and immune escape mutations within the course of single infections [1]. Rates of viral evolution are so rapid that viruses are among the few organisms which can be used to validate the tools used to reconstruct molecular phylogenies [2]. However, at the same time, perhaps more so than for other biological entities, the long-term evolutionary history of viruses is far less well understood. This is, in part, because the rapid mutation rates that enable the study of their short-term evolution erode the signal of molecular evolution in nucleotide sequences [3], but also due to their physical fragility. Thus, the genomic fossil record is the only way to study viral evolutionary history on timescales spanning millions of years.




Recomendo a leitura dessa série especial 'Paleovirology: insights from the genomic fossil record' compilada e editada por Aris Katzourakis. GRÁTIS!