A specific characteristic of infectious disease epidemiology is the definition the different stages of infection according to time.

The starting point is the moment when a pathogen enters the host: this moment is often referred to as 'exposure moment'. Immediately after this moment, the pathogen usually will move to the preferred tissue or target organ. This will be the place within the host where the pathogen can effectively multiply. Different pathogens may have different target organs. Hepatitis virus will target the liver for multiplication, for example, while Legionella will target the lungs.

In the next stage, the pathogen will multiply and the host immune system will start a response. This is the start of the infectious process, where cellular and humoral host defenses will be activated. Though this process may not yet be visible through clinical symptoms, there will be signs that can be observed through laboratory diagnostics ( such as increased sedimentation rate, shift in the distribution of white blood cells). At this stage we may speak of 'an infection' (which may be symptomatic or asymptomatic).

The period between exposure and infection is called 'latent period', since the pathogen is present in a 'latent' stage, without clinical symptoms or signes of infection in the host.

The period between exposure and onset of clinical symptoms is called 'incubation period'.

The host may become infectious (i.e. able to transmit the pathogen to other hosts) at any moment of the infection. This moment will vary per pathogen.

The following schematic figure demonstrates these different time periods:

 

When one person transmits an infection to another, then the time that elapses between onset of symptoms in the primary case and onset of symptoms of the secondary case is called 'generation time', referring to the time it takes for the first group of patients to 'generate' the next group.