This report is an extension of the work of PROTECT Phase 2 and covers the work done under phase 3 of PROTECT, in which researchers from theme 2 of the PROTECT NCS, developed simplified models and introduced two different viral mechanisms and
dose-response models. In this report, researchers extend these existing PROTECT models to account for location in body and infection site incorporating wider research.

This report documents research gaps in dose response and within host modelling. A framework is presented for the viral dynamics in different organs, which is left as a conceptual model due to the limitation of data. In addition, researchers adopt previously developed dose-response models and consider the infectiousness and infectious window.

Good fits to the human challenge data from PROTECT can be seen in two-compartment within host models. For two-compartment models involving nose and throat, different scenarios have been developed. In each scenario, researchers observed the corresponding model can explain the available human challenge
data.

Whilst methods can be derived to explain data available, gaps remain in key processes such as transfer from host to contacts.

Related