Update cross-immunity parameters and appendix

autumn/models/sm_covid2/params.yml

@@ -168,8 +168,8 @@ voc_emergence:
     icu_risk_adjuster: 1.
     cross_protection:
       wild_type: 1.
-      delta: 0.68 # 32% immune escape   DOI: 10.1503/cmaj.211248
-      omicron: .45  # 55% immune escape  DOI: 10.1503/cmaj.211248
+      delta: 0.82  # https://doi.org/10.1016/S0140-6736(22)02465-5
+      omicron: 0.45 # https://doi.org/10.1016/S0140-6736(22)02465-5
   delta:
     starting_strain: false
     seed_prop: 0.
@@ -185,7 +185,7 @@ voc_emergence:
     cross_protection:
       wild_type: 1.
       delta: 1.
-      omicron: .45  # 55% immune escape  DOI: 10.1503/cmaj.211248
+      omicron: .45  # https://doi.org/10.1016/S0140-6736(22)02465-5
   omicron:
     starting_strain: false
     seed_prop: 0.

docs/tex/tex_descriptions/models/sm_covid/stratifications/strains.tex

@@ -7,9 +7,9 @@
 
 We assumed that individuals previously infected with the wild-type strain could only be reinfected with the delta or 
 omicron strains. However, such individuals have a reduced risk of infection with these variants compared to 
-infection-naive individuals (68\% and 45\% reduction for delta and omicron, respectively) \textcolor{red}{[REF DOI: 10.1503/cmaj.211248]}.
+infection-naive individuals (82\% and 45\% reduction for delta and omicron, respectively) \cite{stein2023}.
 We assumed that individuals previously infected with the delta variant could only be reinfected with the omicron variant, 
-with an infection risk reduced by 45\% compared to infection-naive individuals \textcolor{red}{[REF DOI: 10.1503/cmaj.211248]}. 
+with an infection risk reduced by 45\% compared to infection-naive individuals \cite{stein2023}. 
 The other parameters used to represent strain-specific characteristics are presented in Table \ref{param_table}.
 
 Seeding of each new strain into the model was achieved through the importation of a small number (10 per million population) of new infectious persons with the relevant strain into the model.