Stuck in the cell: trapping viruses in infected cells was a frequent adaptation strategy in human hosts

Abstract

Hosts and viruses are in a constant evolutionary arms race, in which viruses physically interact with many host proteins (immune and non-immune) in order to replicate. Here, we manually classify [~]2,500 human virus interacting proteins (VIPs) as a function of their involvement during specific viral replication steps in order to quantify host adaptation across the viral replication cycle. We use an extension of the McDonald-Kreitman test, ABC-MK, to quantify adaptation in human VIPs compared to confounder-matched non-VIPs at different steps of the viral replication cycle. We find significant adaptation at viral replication cycle steps related to entry and release of virions from the cell, with release in particular having experienced extremely high adaptation during human evolution. In contrast to the strategy of host adaptation at entry, which prevents the virus from getting in the cell and replicating in the first place, adaptation at the release stage traps new virions in the cell to prevent continued infection. We explain this unique pattern of adaptation under the framework of a process called intergenerational phenotypic mixing. This adaptation that prevents new viral particles from exiting the cell to continue infection in the host was such a frequent and important strategy in human hosts that the evidence of it can still be found in the form of extremely strong measures of positive selection. Author SummaryViruses have been a powerful driver of evolution throughout human history. Though there have been many studies that have examined the interactions between viruses and the human immune system, few have approached the question from the perspective of what the virus needs from a host cell in order to replicate. As a virus interacts with many host proteins of various functions, whether it is hijacking or suppressing the normal cellular functions of these proteins, identifying adaptation where human hosts defeated viruses in the past may provide key insights that could lead to a better understanding of host-virus interactions, as well as new potential antiviral drug targets. Here, we test for positive selection in manually curated gene sets that span the viral replication cycle in host cells (e.g. entry into the cell, replication, transport within the cell). We identify specifically the step of viral release from the cell, wherein newly assembled viral particles exit an infected cell to go infect another, as a hotspot of extremely elevated adaptation. This result gives new insight into how human hosts defended against viruses in the past and identifies specific functional classes of proteins that were the targets of repeated, strong adaptation.