Enhancing global preparedness during an ongoing pandemic from partial and noisy data

As the coronavirus disease 2019 spread globally, emerging variants such as B.1.1.529 quickly became dominant worldwide. Sustained community transmission favors the proliferation of mutated sub-lineages with pandemic potential, due to cross-national mobility flows, which are responsible for consecutive cases surge worldwide. We show that, in the early stages of an emerging variant, integrating data from national genomic surveillance and global human mobility with large-scale epidemic modeling allows to quantify its pandemic potential, providing quantifiable indicators for pro-active policy interventions. We validate our framework on worldwide spreading variants and gain insights about the pandemic potential of BA.5, BA.2.75, and other sub- and lineages. We combine the different sources of information in a simple estimate of the pandemic delay and show that only in combination, the pandemic potentials of the lineages are correctly assessed relative to each other. Compared to a country-level epidemic intelligence, our scalable integrated approach, that is pandemic intelligence, permits to enhance global preparedness to contrast the pandemic of respiratory pathogens such as SARS-CoV-2.

Automated summary

As the coronavirus disease 2019 spread globally, emerging variants like B.1.1.529 quickly became dominant worldwide. Sustained community transmission and cross-national mobility flows led to consecutive cases surge. Integrating data from national genomic surveillance and global human mobility with epidemic modeling allows quantifying the pandemic potential of emerging variants and provides indicators for policy interventions. This scalable integrated approach enhances global preparedness to counter the pandemic of respiratory pathogens.