Multi-strain dynamics

Question 1

strain

Answer 1

the genetic loci that encode the antigens against which immunity acts

Question 2

allelic sequence

Answer 2

allele at each locus

Question 3

cross immunity assumptions

Answer 3

reduces transmission of strains that share immune targets

Question 4

Why do multi-strains behave similarly in SIR-like models ?

Answer 4

• same epidemiological parameters
• yamma = 0 (no strain structure)
• all strains have similar success/dyanmics
• their differences are attributable to their starting conditions
• extract prevalence statistics to check

Question 5

Increasing beta in one strain when gamma = low

Answer 5

• changes R0
• higher, more frequent epidemics initially
• higher prevalence at eqm
• behaviour is quantitatively different, but qualitatively the same

Question 6

measuring strain diversity per time step [when?]

Answer 6

• diversity is higher when strains are co-circulating at a similar prevalence
• diversity increases with epidemics
• plateus at eqm

Question 7

If gamma is high, but beta is the same [check this]

Answer 7

• discrete strain structure
• strains transmit the same

Question 8

prevalence data high-gamma classifications

Answer 8

high dominant prevalence, intermediate subdominant prevalence, low exclusion/extinction level

Question 9

Why do high-gamma multi-strain dynamics lead to segregation?

Answer 9

• initial chaotic epidemic period is unpredictable
• cross-immunity forces system to self-organise after dominance is established

Question 10

Predictions of a multi-strain dynamical system with high gamma

Answer 10

1) strains that share alleles with the dominant strain will be driven to extinction via herd immunity
2) different alleles co-circulate at intermediate prevalence, but compete with each other for susceptible, limiting their growth

Question 11

editing beta in high gamma models

Answer 11

high beta becomes dominant

Question 12

Measuring strain diversity per time step in high gamma models

Answer 12

1) initial diversity oscillations
2) diversity and systems converge on eqm
3) extinction = low diversity

Question 13

intermediate gamma, same beta systems

Answer 13

• chaotic strain structure
• intermediate dynamics avoid eqm
• SIR framework delivers recurrent epidemics
• epidemic establishment creates herd immunity for other strains, suppressing them
• interference from similar strains limits immunity in pop; susceptible retained

Question 14

chaotic strain structure and influenza

Answer 14

• many sequential strains
• next epidemic unpredictable
• impacts vaccines

Question 15

Differences in host reservoir lifespan?

Answer 15

shorter lifespan leads to:
- higher peaks more regularly
- faster cycling due to host turnover
- higher diversity

Question 16

Measuring strain diversity per time step in intermediate models

Answer 16

• diversity oscillates; unstable
• each epidemic caused by a single strain
• low diversity

Question 17

Strain control of beta under high gamma

Answer 17

• you can control the dominant strain, the subdominant strain, or none
• introduces extra parameters

Question 18

subdominant control

Answer 18

• subdominant tends to extinction
• rise to dominance and increased prevalence of a competitor

Question 19

dominant control

Answer 19

• dominant tends to extinction
• subdominant release
• codominance of non-interfering strains