2: R and All That - Basic Concepts of the Epidemiology of Infectious Diseases

Question 1

incubation period

Answer 1

time between the moment someone is infected and the moment they exhibit symptoms

Question 2

generation time

Answer 2

time between the moment someone is infected and the moment they infect someone else

always greater than 0 since you cannot infect someone else before you are infected

invisible process and hard to accurately measure

Question 3

serial interval

Answer 3

time between the moment a person A, who had infected a person B, exhibits symptoms and the moment B exhibits symptoms

time that elapsed between the moment you have symptoms and the moment they have symptoms when you are the one who infected them

can be smaller than 0 since you can be infectious before you exhibit symptoms

Question 4

basic reproduction number (R0)

Answer 4

average number of people that someone who is infected would go on to infect in a population where everyone is susceptible (purely hypothetical situation)

estimated from the growth rate of the epidemic

not an intrinsic property of the virus because it doesn’t just depend on the virus’ biological properties but other factors like populations, cultures, behaviour, population densities, etc.

Question 5

effective reproduction number (Rt)

Answer 5

average number of people a person who is infected at time t will go on to infect

different from R0 because it refers to the actual situation at a given time and not a hypothetical situation where everyone is susceptible

when > 1, epidemic is growing
when < 1, epidemic is receding so if it stays like that for long enough, the epidemic is less of a concern

Question 6

dispersion factor

Answer 6

parameter k that measures how concentrated on a few people transmission events are

measures how equal or unequal secondary infectious are

the lower k is, the more a small number of people are responsible for a greater share of secondary infections

Question 7

epidemic growth rate (r)

Answer 7

(number of infections at time t + 1 / number of infections at time t) - 1
- expressed in percentage terms

don’t observe infections but only diagnosed cases however when under reasonable assumptions (short periods of time) it doesn’t change or matter for the rate of growth
- about the share of the cases you detect staying constant

so as long as the rate at which you detect cases doesn’t change, you get the growth rate which is pretty close to the growth rate of the actual number of infections

Question 8

relationship between rate of growth (r) and effective reproduction number (R)

Answer 8

use r to infer R
- need to use some equation to relate the reproduction number to growth rate, and to know what equation to use, need to know what the distribution of the generation time looks like

typically the case that r is inversely related to the average generation time

• the shorter the generation time, the larger the growth rate keeping R equal
• the higher R is , the larger the growth rate keeping the general time equal

R and not r that determines the size of a wave
- r still important since it overwhelms hospitals faster

Question 9

epidemic doubling time

Answer 9

how much time it would take for the cumulative number of infections to double if the epidemic grew at a constant rate

ln(r)/2