From Book 1: Universe (pg240), you should fill a health box for each disease point obtained, which stacks with damage points obtained (ticked). Disease points are harder to remove though, and if not taken care of, will quickly kill your character in a few days.
It actually gets worse, you cannot recover damage points if ill and wounded, meaning you are in a spiral to your death if you ignore it, some diseases can kill you after a couple of days unless you treat your wounds and rest, while weak diseases will, at most, cause an extra 5 points of damage that cannot be healed until the time has passed.
There are 4 types of diseases in the system, called Virulance Levels:
Weak: Difficult Threshold (11), Disease Points 5 (1/day)
Mild: Difficult Threshold (14), Disease Points 10 (2/day)
Malignant: Difficult Threshold (17), Disease Points 15 (3/day or death)
Deadly: Difficult Threshold (20), Disease Points 20 (4/day or death)
This defines the amount of Disease Points you get while ill and the difficult to heal it through spells
Disease Points
The effects of a disease are simulated by Disease points, which worsen
the Character’s Health Condition. The Player fills the necessary
number of boxes in her Health Condition chart as the sickness wears
on. Damage points and Disease points stack, which can turn dangerous
for the PC. Diseases of Malignant and Deadly Virulence may inflict no
Disease points, resulting in instant death instead. Only a very
skilled physician (see below) or a mystical power (Demorthèn or from
the Temple) can then save the patient.
Duration
In most cases, a disease lasts five days, during which the Character
suffers a certain amount of daily Disease points (1 point if the
disease is weak, 2 if it is mild, 3 if it is malignant and 4 if it is
deadly). In the case of diseases of Malignant or Deadly Virulence that
can kill, death occurs at the end of these five days. Some diseases
can evolve in a faster or slower way than the average; the Leader
divides the amount of Disease points by the number of days the illness
lasts (see the previous chart). For example, a Malignant disease
lasting only 3 days will inflict 5 daily Disease points.
Diagnosis
Diagnosing an illness requires a Standard (11) Medicine roll. A
natural 1 on this roll means a wrong diagnosis, whereas a regular
failure simply means the Character cannot identify the disease. A
success gives the Virulence of the illness and ideas for adequate care
(see on the following page).
And finally
Resting and Recovering
Resting can often allow a Character to recover from a disease, even a
dangerous one. She needs to rest as long as it is in effect, and she
will suffer the appropriate Disease points for its Virulence. However,
she will recover all of those points the day after the end of her
disease. If a Character does not rest, the disease may live on after
its normal five day duration; in that case, on the sixth day, the
patient has to make a Stamina roll related to the Virulence. A failure
means that the illness persists and deals the same number of daily
Disease points again (another Stamina roll must be made the following
day); a critical failure leads to death. A success means a remission
and a recovery from all the Disease points. When a Character is ill
and wounded, she cannot recover damage points due to injuries by
resting. Only medical care can allow it, but at the rate of one daily
Health point instead of the normal two.
Also, a character with the Medicine Skill can roll a Complicated check (14) to reduce the amount of Disease Points obtained by 1, but you must be resting all day. If the disease will kill a character instead of causing disease points, the Medicine check can save him with a (17) roll.
