Epidemiological indices with multiple circulating pathogen strains

Epidemiological indicators, such as reproduction numbers and epidemicity indices, describe an ongoing epidemic’s long- and short-term behaviour. Their evolving values provide context for designing control measures, as maintaining both indices below one warrants a waning epidemic. However, current models for the computation of epidemiological metrics do not consider the pathogen stratification into variants endowed with different infectivity and epidemiological severity, as was the case with SARS-CoV-2. Failing to account for such stratification prevents the resulting epidemiological indices from spotting the possible onset of uncontrolled growth of one variant within the total of new infections, thus limiting the prognostic value of the indicators. Here, we expand an existing framework for the computation of spatially explicit reproduction numbers and epidemicity indices to account for arising variants. By contrasting the data of the COVID-19 pandemic in Italy, we show that embedding additional layers of complexity in the mathematical model reveals epidemiological metrics at the emergence of new variants significantly exceeding their threshold. Such values foresee a recrudescence in new infections that only became evident after emerging variants effectively replaced the previous strains. These higher values flag the presence of a specific variant that grows more rapidly than the growth of the total number of infections generated by all variants combined. Variant-stratified epidemiological indicators do therefore allow control measures to be better tailored to the shifting severity of an ongoing epidemic.