Infectious Disease Modelling

Question 1

What is the SIR Model for Infectious Diseases

Answer 1

Susceptible –> Infected –> Recovered

Everyone is allocated to 1 box, can’t be in more than 1.

Question 2

What is R0

Answer 2

the average number of secondary infections caused by a single typical infectious individual over their lifetime when introduced to a completely susceptible population (depends on both pathogen and population)

Question 3

What is Re or Rt
(Net/Effective Reproduction Number)

Answer 3

Takes into account the current state of the population:
- not everyone is susceptible (some people are immune etc.)
- changes in contact rate
- If 1 infection is in reality causing <1 case: good.

Question 4

What is herd immunity

Answer 4

A population is protected when not everyone is immune
(most people are immune so Re (or Rt) is <1).

Question 5

What happens in the growth phase
What is generation time

Answer 5

Exponential Growth.
Generation Time = mean time interval between infection and the onwards infections they cause <– if known can give data about R0.
Need to know R0 and Generation Time because otherwise exponential growth can either be a big R0 and small generation time or a small R0 and big generation time
Contact tracing can help estimate

Question 6

Turnover

Answer 6

when stops being exponential and starts decreasing (reaches a peak)

Question 7

SI Model

Answer 7

Susceptible –> Infected

never stop being infected e.g. HIV

If R0 = 2: will stop infecting when 1/2 population is infected.
If R0 = 4 or 5: theoretically will only cause infection when 75-80% of population infected (but in HIV this doesn’t actually happen due to heterogeneity –> a core group e.g. those with lots of sexual partners will have high prevalence but this is usually a small fraction of the population

Question 8

SIS Model

Answer 8

Susceptible –> Infected –> Susceptible
e.g. Gonorrhoea, Rhinovirus

Question 9

SIRS Model

Answer 9

Susceptible –> Infected –> Recovered –> Susceptible

Stay immune for a while but it wanes e.g. pertusis

Question 10

SEIR Model

Answer 10

Susceptible –> Exposed –> Infected –> Recovered

Exposed = latent infection. Allows to build a delay in modelling between infection and infectiousness. Useful for contact tracing and quarantine

Question 11

What happens after infection spike is over (endgame)

Answer 11

Following a decline & reaching endemicity, children or immigration can increase numbers again. –> the higher the birth rate the smaller the interval between peaks