By definition, when a new pathogen genotype appears through mutation in a population it is very rare.
Stochasticity. The rarity of the pathogen implies that its population dynamics are difficult to predict due to stochastic forces. Put differently, the ’classical‘ models that assume deterministic dynamics are inadequate.
‘Evolutionary rescue’. Dynamics of rare mutants have become very popular to study how a population can cope with a sudden environmental. If nothing changes, the population will go extinct with certainty, but if it evolves, i.e. if a mutant emerges and spreads, the population can survive. The latter scenario is called evolutionary rescue.
Epidemiological emergence. Many pathogens are facing certain extinction, e.g. with the implementation of massive public health policies (e.g. mass vaccination). In this situation, evolutionary rescue captures a process by which pathogen evolution allows it to avoid extinction. The interesting aspect of this scenario is that the pathogen population dynamics are very well known (this is classical epidemiologicy). We studied this in the context of the Chikungunya virus (CHIKV) outbreak in La Réunion island in 2005-2006 (Hartfield & Alizon 2014).
Within-host emergence. Inside a host, parasites face many constrainsts but one of the biggest is the activation of the immune response. Again, this is an evolutionary rescue situation because thanks to rapid evolution the parasite population can persist by coping with host immunity. This raises a technical challenge because host immunity is a function of parasite densities. For further details, see Hartfield & Alizon (2015).For further details, see our publications »