Phylodynamics

Phylodynamics is a term coined to describe behavior resulting from the combination of evolutionary and ecological processes.

The rapidly evolving nature of viruses exhibit phylodynamics because their ecological and evolutionary dynamics occur on the same time scale. This means viruses can potentially generate new mutations and adaptations during ecological change in contrast to vertebrates which must rely on pre-existing genetic variation maintained by the population to adapt to the environment. Due to phylodynamics, populations of viruses can adapt to changing environments within a short time frame, sometimes as short as a few days. The rapid change in the genetic makeup of the virus over a short time makes viruses ideal for study using dynamical models (see Mathematical model). The development of better quality viral genome sequences, increased computing power, and sophisticated statistical analysis has increased the power of dynamical models to glean conclusions from viral genetic data.

The role of human movement in Influenza A phylodynamics has been studied via evolutionary analysis of thousands of Influenza A genomes. Historically, Influenza A acts in cycles, causing high mortality in very short periods of time in a predictable pattern. Analysis of the viral genetic data revealed although the virus evolved rapidly over time, it has limited diversity across several continents. This suggests the variants of the individual strains of Influenza A all descended from a common ancestor The model also revealed the common ancestor was a Southeast Asian source and the virus is spread worldwide by global air flight patterns. This pattern accounts for the cyclical nature of Influenza A pandemics happening in the winter and dying out by summer time.

Phylodynamic modeling has also been used to reconstruct transmission histories. For example, analysis of the 2001 foot and mouth disease outbreak in the United Kingdom was used to construct a transmission chain of the disease spread by studying the infection process at individual farms. Farm to farm transmission was discovered to be facilitated by transport of infected livestock. This transmission history model was then used to develop a model that provided a probability distribution for the date of infection of each farm and the likely period of infectiousness before a diagnosis was made. Viral genetic data collected from the infected farms was then analyzed to identify the most likely chains of virus spread. This genetic analysis revealed a clear path with which the virus traveled from farm to farm by correlating the movement of the virus over time. This was possible because the rapid spread of foot and mouth disease meant little genetic change occurred during farm to farm transmission.

The ability to simultaneously look at the global dynamics of many viruses side by side has led to some emerging insights. Viruses that display the most complex global dynamic behavior tend to be highly transmissible viruses that cause acute (medicine) infections in short lived epidemics. Looking at human viruses that exhibit this type of behavior, e.g. enteroviruses (i.e. polio), rhinoviruses (i.e. common cold), caliciviruses, and paramyxoviruses (i.e. mumps), it seems likely that the complex dynamic behavior is a result of interaction between transmission ability, host herd immunity and viral adaptation. This pattern of behavior can be used as a rough means of estimating the potential pandemic inducing power of new viruses or new strains of old viruses. For example, when H1N1 was first detected in April of 2009, the analysis of its genome showed a high potential for inducing human pandemics. This early warning of potential trouble was essential in the development of public health protocols such as infection management and control, vaccine development, and so forth.