Principles of dengue virus evolvability derived from genotype-fitness maps in human and mosquito cells

Abstract

Dengue virus (DENV), an arbovirus infecting over 100 million annually, cycles between human and mosquito hosts1. Examining how DENV adapts to such different host environments could uncover principles of arbovirus transmission and emergence. Here we combine sequential passaging and ultra-deep sequencing to examine the sequence dynamics and fitness changes of DENV populations adapting to human and mosquito cells, identifying the contributions of beneficial and deleterious mutations in shaping the fitness landscape driving host-specific paths of viral adaptation. We find DENV phenotypic adaptation is best described by the collective fitness contributions of all the alleles present in the population. Accordingly, while increased fitness during adaptation to each host is driven by host-specific beneficial mutations, it is reduced by the consistently replenished genetic load of deleterious mutations. Of note, host-specific beneficial mutations are in discrete regions across the genome, revealing molecular mechanisms of adaptation. Some of these clusters comprise phenotypically redundant mutations that may provide evolutionary robustness to transmission bottlenecks. Our results also suggest DENV adaptation is facilitated through variation in intrinsically disordered protein regions while transmembrane and structured domains evolve under stronger biophysical constraints. Importantly, the adaptation strategies uncovered in our simple system mirror macro-evolutionary changes observed across DENV serotypes and Zika virus and may suggest general principles of evolvability in arbovirus evolution.