New study of evolutionary rates in viruses

Sebastian Duchene and Simon Ho, together with colleague Eddie Holmes, have published a paper on viral evolutionary rates in Proceedings of the Royal Society of London B. This paper has important implications for our understanding of the evolutionary rates and timescales of viruses.

Viruses are responsible for a large proportion of infectious diseases. They can spread through populations very rapidly and are often capable of evading the immune response of their hosts. In some cases, viruses can infect different host species, leading to outbreaks that are difficult to control. These remarkable features of viruses are attributed to the fact that they evolve much more rapidly than cellular organisms. For example, the genomes of influenza viruses mutate about a million times more rapidly than those of mammals.

The paper presents a comprehensive analysis of evolutionary rates in viruses, a topic that has attracted considerable attention in recent years. Knowledge of viral mutation rates is essential for estimating their evolutionary timescales using genetic methods. This approach is frequently used to date important events such as the current HIV pandemic and the origins of recent influenza outbreaks.

Sebastian and colleagues performed computational analyses of over 100 viruses. The most important result of the study is that estimates of evolutionary rates have biases that vary with the timescale of observation. For example, viruses seem to evolve much more rapidly over a few months within a host than over thousands of years across different species. This causes major difficulties for our understanding of virus evolution because it can lead to enormous biases in estimates of evolutionary timescales. As a consequence, there has been little consensus over the timescale over which viruses evolve. In fact, some viruses may be thousands of years older than our current estimates.

Using detailed analyses of HIV data, Sebastian and colleagues were able to pinpoint some of the causes of rate variation. They found that natural selection is a major factor, being strong enough to operate over very short timescales. Virus samples collected over a short timeframe have high rates of evolution because they include lineages that will survive only for a short time. In contrast, viruses collected over a long timeframe do not include these short-lived lineages, so the rate of evolution appears low.

The implication of this study is that viral evolution needs to be reconsidered as a much more dynamic process. Some factors, such as natural selection, have effects that depend on the timescale of study. New models and computational techniques need to be developed to account for the evolutionary factors that shape virus diversity.

Read the scientific publication here:
Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates
Duchene, Holmes, Ho (2014) Proceedings of the Royal Society B, 281: 20140732