Covariate derivation

Model structure classification

Human raters classified models according to methodological structures.

Table 1: Classification of models by number of raters in total and agreement on model structure.
Model Final classification Agreement Total raters Semi-mechanistic Mechanistic Agent-based Statistical Judgement Other Machine Learning
AMM-EpiInvert Statistical FALSE 3 0 0 0 2 0 1 0
DSMPG-bayes Semi-mechanistic FALSE 3 2 0 0 1 0 0 0
ILM-EKF Semi-mechanistic FALSE 3 2 0 0 1 0 0 0
ITWW-county_repro Semi-mechanistic FALSE 3 2 0 0 1 0 0 0
Imperial-DeCa Semi-mechanistic FALSE 3 2 0 0 1 0 0 0
Imperial-RtI0 Semi-mechanistic FALSE 3 2 0 0 1 0 0 0
Imperial-sbkp Semi-mechanistic FALSE 3 2 0 0 1 0 0 0
KITmetricslab-bivar_branching Statistical FALSE 3 1 0 0 2 0 0 0
Karlen-pypm Mechanistic FALSE 3 0 2 0 1 0 0 0
LANL-GrowthRate Semi-mechanistic FALSE 3 2 0 0 1 0 0 0
SDSC_ISG-TrendModel Statistical FALSE 3 0 0 0 2 0 1 0
UMass-SemiMech Semi-mechanistic FALSE 4 3 1 0 0 0 0 0
USC-SIkJalpha Mechanistic FALSE 4 1 3 0 0 0 0 0
UpgUmibUsi-MultiBayes Semi-mechanistic FALSE 3 2 0 0 1 0 0 0
bisop-seirfilter Mechanistic FALSE 4 1 3 0 0 0 0 0
bisop-seirfilterlite Mechanistic FALSE 4 1 3 0 0 0 0 0
prolix-euclidean Semi-mechanistic FALSE 4 3 0 0 0 0 1 0
CovidMetrics-epiBATS Statistical TRUE 3 0 0 0 3 0 0 0
EuroCOVIDhub-baseline Statistical TRUE 4 0 0 0 4 0 0 0
FIAS_FZJ-Epi1Ger Mechanistic TRUE 3 0 3 0 0 0 0 0
GoeWroc-BaseBayes Semi-mechanistic TRUE 3 3 0 0 0 0 0 0
HZI-AgeExtendedSEIR Mechanistic TRUE 3 0 3 0 0 0 0 0
ICM-agentModel Agent-based TRUE 3 0 0 3 0 0 0 0
IEM_Health-CovidProject Mechanistic TRUE 4 0 4 0 0 0 0 0
JBUD-HMXK Mechanistic TRUE 3 0 3 0 0 0 0 0
LeipzigIMISE-SECIR Mechanistic TRUE 3 0 3 0 0 0 0 0
MIMUW-StochSEIR Mechanistic TRUE 3 0 3 0 0 0 0 0
MIT_CovidAnalytics-DELPHI Mechanistic TRUE 3 0 3 0 0 0 0 0
MOCOS-agent1 Agent-based TRUE 3 0 0 3 0 0 0 0
MUNI-ARIMA Statistical TRUE 3 0 0 0 3 0 0 0
MUNI-LaggedRegARIMA Statistical TRUE 3 0 0 0 3 0 0 0
MUNI-VAR Statistical TRUE 3 0 0 0 3 0 0 0
MUNI_DMS-SEIAR Mechanistic TRUE 3 0 3 0 0 0 0 0
PL_GRedlarski-DistrictsSum Mechanistic TRUE 3 0 3 0 0 0 0 0
RobertWalraven-ESG Statistical TRUE 3 0 0 0 3 0 0 0
UB-BSLCoV Statistical TRUE 3 0 0 0 3 0 0 0
UC3M-EpiGraph Agent-based TRUE 3 0 0 3 0 0 0 0
ULZF-SEIRC19SI Mechanistic TRUE 3 0 3 0 0 0 0 0
UMass-MechBayes Mechanistic TRUE 3 0 3 0 0 0 0 0
UNED-PreCoV2 Statistical TRUE 3 0 0 0 3 0 0 0
UNIPV-BayesINGARCHX Statistical TRUE 3 0 0 0 3 0 0 0
epiMOX-SUIHTER Mechanistic TRUE 3 0 3 0 0 0 0 0
epiforecasts-EpiExpert Judgement TRUE 3 0 0 0 0 3 0 0
epiforecasts-EpiExpert_Rt Judgement TRUE 3 0 0 0 0 3 0 0
epiforecasts-EpiExpert_direct Judgement TRUE 3 0 0 0 0 3 0 0
epiforecasts-EpiNow2 Semi-mechanistic TRUE 3 3 0 0 0 0 0 0
epiforecasts-weeklygrowth Statistical TRUE 2 0 0 0 2 0 0 0
itwm-dSEIR Mechanistic TRUE 3 0 3 0 0 0 0 0

Epidemic trend identification

We categorised each week as “Stable”, “Decreasing”, or “Increasing”, based on the difference over a three-week moving average of incidence (with a change of +/-5% as “Stable”).

Variant phase identification

Genomic surveillance data were obtained from three sources: ECDC (covering 30 European countries), UKHSA (Great Britain), and the Swiss Federal Office of Public Health (Switzerland). Variant lineages were mapped to six named phases in expected chronological order: Alpha, Delta, Omicron-BA.1, Omicron-BA.2, Omicron-BA.4/5, and Omicron-BQ/XBB. For each country, we identified the first week in which each named variant exceeded 50% of sequenced samples. We enforced chronological ordering by removing any out-of-sequence phases, then expanded phase assignments to all weeks by filling forward and backward from observed transition dates. This per-location approach accounts for the fact that variant dominance dates differed substantially across European countries. Where genomic surveillance data were too sparse to identify a transition (Hungary), we supplemented with epidemiological reports to set the Alpha-to-Delta transition date.

Figure 3: Variant phases identified by dominant variant in each location and week