Rapid emergence of clonal interference during malaria parasite cultivation

Abstract

Laboratory cultivation of the malaria parasite Plasmodium falciparum has underpinned nearly all advances in malariology in the past 30 years. When freshly isolated clinical isolates are adapted to in vitro culture mutations rapidly fix increasing the parasite growth rate and stability. While the dynamics of culture adaptation are increasingly well characterized, we know little about the extent of genomic variation that arises and spreads during long term culture. To address this we cloned the 3D7 reference strain and maintained a culture for ~84 asexual cycles (167 days). Growth rate of the culture population increased 1.14-fold over this timeframe. We used single cell genome sequencing of parasites at cycles 21 and 84 to measure the accumulation of diversity in vitro. This parasite population showed strong signals of adaptation across this time frame. By cycle 84 two dominant clades had arisen and were segregating with the dynamics of clonal interference. This highlights the continual process of adaptation in malaria parasites, even in parasites which have been extensively adapted to long term culture.

A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations

“…Clonal interference has been shown to emerge rapidly in laboratory cultivated P. falciparum , where the parasite cycles through only asexual stages, suggesting it may influence the dynamics of the emergence of resistance ( Jett et al, 2020 ). The evolutionary model used here may therefore overestimate the fixation probability of mutations with milder beneficial effects and underestimate the fixation probability of mutations with larger beneficial effects ( de Visser and Krug, 2014 ).…”

A computational method for predicting the most likely evolutionary trajectories in the step-wise accumulation of resistance mutations

“…This can lead to a process known as ‘greedy adaptation’, in which the mutation of larger beneficial effect is fixed with certainty ( Jain et al, 2011 ). Clonal interference has been shown to emerge rapidly in laboratory cultivated P. falciparum , where the parasite cycles through only asexual stages, suggesting it may influence the dynamics of the emergence of resistance ( Jett et al, 2020 ). The evolutionary model used here may therefore overestimate the fixation probability of mutations with milder beneficial effects and underestimate the fixation probability of mutations with larger beneficial effects ( de Visser and Krug, 2014 ).…”