Katia Koelle

The paper investigates how spatial expansion and dispersal modulators affect viral population structure and genetic diversity during infection.

This study shows bovine-derived H5N1 viruses face evolutionary constraints in ferrets, limiting adaptation for efficient mammalian transmission despite robust replication.

This study shows environmental stochasticity can explain within-host viral evolution patterns without needing demographic stochasticity or constant population size assumptions.

This study quantifies how pre-existing tissue-resident CD8 T cells reduce donor infectiousness in a mouse model of respiratory virus transmission.

The paper shows that assuming an exponential generation interval in phylodynamic inference leads to underestimation of the reproduction number R during early epidemic growth.

This study examines within-host evolutionary dynamics of influenza A virus in humans and ferrets, finding that genetic drift limits selection efficiency in humans but not in ferrets.

This study quantifies genetic drift in within-host influenza virus populations using a population genetic model, finding low effective population sizes and evidence against the Wright-Fisher model in swine infections.

This paper develops a framework to estimate pandemic potential from experimental transmission studies by analyzing within-host viral dynamics and extrapolating to epidemiological parameters.

ScTree improves scalability and accuracy of phylodynamic models for transmission tree inference by using a Bayesian framework with infinite-sites mutation modeling.

This study investigates how incomplete purifying selection affects viral phylogenies and phylodynamic inference, finding little bias in key epidemiological estimates despite mutation distribution shifts.

This study shows that dispersal within the respiratory tract affects viral genetic diversity and evolutionary potential, with nasal and tracheal regions maintaining diversity while lung regions show genetic distinctness.

The paper explains how waning immunity drives antigenic evolution in respiratory viruses through repeated emergence and replacement of immune escape variants.

This study uses simulations to show that immune pressure, not just replicative fitness, explains observed viral evolution patterns in prolonged infections.

This study uses full genome SARS-CoV-2 sequences from Israel to trace viral spread, find multiple introductions, and show the impact of social distancing on transmission.