Objective 1: I have studied the dynamics of antibiotic resistant and sensitive strains within a host during and after antibiotic treatment. I was particularly interested whether different types of antibiotics (biostatic antibiotics inhibit cell growth, biocidic antibiotics actively kill bacterial cells) have a different effect on the process of resistance evolution and proliferation. It turns out that they indeed affect the process differently, e.g. the carriage time of resistant bacteria in a host after treatment is much increased by treatment with bactericidal antibiotics. This work is still ongoing and I aim to finish a manuscript by the end of Summer 2021.
Objectives 2 and 3: Due to the shift in research questions, I did not have the time to work on these objectives.
(A) We studied a within-host dynamical model of virus dynamics and estimated the effect of prophylactic treatment with different types of antiviral drugs that differ in their mechanism of action, e.g. antivirals that attack the virus before it has infected susceptible target cells or antivirals that inhibit the production of new virus particles in infected target cells. We computed the efficacy for the different drug types to completely inhibit the establishment of a viral infection. Even if infection cannot be prevented entirely, prophylactic treatment can still delay infection establishment and by that "flatten the viral load curve" within hosts. The results of this work are published in the scientific journal PLoS Computational Biology.
(B) We have developed an epidemiological model that reflects the disease progression of COVID-19 in a population. Specifically, we accounted for a transmission rate that varies over the age of infection of infected individuals. With this model, we then estimated the effective reproduction number in France in Spring 2020. A manuscript summarising the results is published on the arXiv preprint server.
(C) We modeled the early epidemic dynamics of a local infection cluster. With this model, a special case of the model developed in (B), we for example estimated that the SARS-CoV-2 variant of concern B.1.1.7 detected (retrospectively) in September 2020 in the UK first appeared in the UK early August 2020. Last, we estimated a minimal testing frequency to detect clusters before they exceed a certain threshold size.
As a result of my COVID-19-related work, I was invited to seminars at the Frankfurt Institute of Advanced Sciences to talk about project (A), at the University of Helsinki and to the Biohasard workshop in Grenoble to talk about project (C) (all online seminars).
