Adaptation to host cell environment during experimental evolution of Zika virus

Abstract Zika virus (ZIKV) infection can cause developmental and neurological defects and represents a threat for human health. Type I/III interferon responses control ZIKV infection and pathological processes, yet the virus has evolved various mechanisms to defeat these host responses. Here, we established a pipeline to delineate at high-resolution the genetic evolution of ZIKV in a controlled host cell environment. We uncovered that serially passaged ZIKV acquired increased infectivity, defined as the probability for one virus to initiate infection, and simultaneously developed a resistance to TLR3-induced restriction. We built a mathematical model that suggests that the increased infectivity is due to a reduced time-lag between infection and viral replication. We found that this adaptation is cell-type specific, suggesting that different cell environments may drive viral evolution along different routes. Deep-sequencing of ZIKV quasi-species pinpointed mutations whose increased frequencies temporally coincide with the acquisition of the adapted phenotype. We functionally validated a point-mutation in ZIKV envelope (E) protein recapitulating the adapted phenotype. Its positioning on the E structure suggests a putative function in protein refolding/stability. Altogether, our results uncovered ZIKV adaptations to the cell environment leading to an accelerated replication onset coupled with resistance to TLR3-induced antiviral response. Our work provides insights into viral escape mechanisms and interactions with host cell and can serve as a framework to study other viruses. Significance Statement Zika virus poses a major threat to Human health worldwide. To understand how Zika virus interacts with human cells, we studied its evolution in cell cultures. We found that the viruses adapted by initiating their replication sooner after cell entry. We sequenced the genomes of the viruses evolved over time and found mutations underlying the adaptation of the virus. One mutation in the envelope viral protein is sufficient to reproduce the faster initiation of replication. Our multidisciplinary approach based on analyzing viral evolution in a controlled environment and mathematical modeling revealed how Zika virus can escape antiviral responses, and can serve as framework to study other viruses.