disease progression dynamics

[slwu89]

IBM - (From @smitdave)
States:

• alpha_i = AoI, for each type
• MoI = # types currently present in the infection
• P_i = log10 parasite densities for each type
• G_{i,j} = micro/macro gametocyte densities of each type
• k = net infectiousness
• C = chemo-protected status
• phi_1 = primary fever status
• phi_2 = secondary fever status
• w = tracking variables
• iron levels / anemia

Other Variables:

• health states: no disease, subjective fever, clinical malaria, severe malaria
• iron levels (which determine anemia)
• exposure tracking variables are updated based only on simple rules, such as total FoI, recent FoI, total EIR, recent EIR, total days infected, ....
• a list of specific types seen

Primary Event: Infection Clears:

• at the moment a parasite infection occurs, record t_0, the age of each infection, alpha_i = t-t_0

A: when will each parasite clear.

• A1: upon infection, draw t_end for each parasite from a pdf;
• A2: t_end be determined dynamically, by the set of rules for updating P (see B: below)

B: Update Rule for P: every day: (P=log10 parasite densities)

• Simple: P_i,t = f(alpha_i), if C=1, end infection
• auto-correlated: P_i,t = f(alpha_i, P_{i,t-1}, C); if P_i<1, end infection
• Interaction: P_t = f(\alpha_i, vec P, ...), if P_i < 1, end infection

G: Update Rule for G: every day:

• Simple: G_{i,j,t} = f_(G_{i,j,t-1}, P_i,t-1), if C=1 and anti-gametocyte activity, then end G.
• k = F_k (G, ...)

phi_1: primary fever

• Upon infection, determine whether a primary fever occurs, and the day on which it will begin
• If a primary fever occurs, determine when treatment will be triggered

phi_2: secondary fever

• Add up B = 10^P_i, and compute probability of fever F_2(B,...)
• If a secondary fever occurs, determine whether to treat it tomorrow

w: update tracking variables
C: Treatment

• Trigger treatment at random
• Simple: If treatment is triggered, set C=1
• Harder: partial treatment / partial compliance

Detection:

• Draw nb. for each P_i
• Draw nb for B