Susceptibility to Zika virus in a Collaborative Cross mouse strain is induced by Irf3 deficiency in vitro but requires other variants in vivo

Zika virus (ZIKV) is a Flavivirus responsible for recent epidemics in Pacific Islands and in the Americas. In humans, the consequences of ZIKV infection range from asymptomatic infection to severe neurological disease such as Guillain-Barré syndrome or fetal neurodevelopmental defects, suggesting, among other factors, the influence of host genetic variants. We previously reported similar diverse outcomes of ZIKV infection in mice of the Collaborative Cross (CC), a collection of inbred strains with large genetic diversity. CC071/TauUnc (CC071) was the most susceptible CC strain with severe symptoms and lethality. Notably, CC071 has been recently reported to be also susceptible to other flaviviruses including dengue virus, Powassan virus, West Nile virus, and to Rift Valley fever virus. To identify the genetic origin of this broad susceptibility, we investigated ZIKV replication in mouse embryonic fibroblasts (MEFs) from CC071 and two resistant strains. CC071 showed uncontrolled ZIKV replication associated with delayed induction of type-I interferons (IFN-I). Genetic analysis identified a mutation in the Irf3 gene specific to the CC071 strain which prevents the protein phosphorylation required to activate interferon beta transcription. We demonstrated that this mutation induces the same defective IFN-I response and uncontrolled viral replication in MEFs as an Irf3 knock-out allele. By contrast, we also showed that Irf3 deficiency did not induce the high plasma viral load and clinical severity observed in CC071 mice and that susceptibility alleles at other genes, not associated with the IFN-I response, are required. Our results provide new insight into the in vitro and in vivo roles of Irf3, and into the genetic complexity of host responses to flaviviruses.Author summary: Recent ZIKV outbreaks led to millions of infected people, with rare but severe complications such as Guillain-Barré syndrome and encephalitis in adults suggesting that host genes influence the susceptibility to severe forms of infection. We previously reported the importance of host genes in ZIKV pathogenesis using a panel of genetically diverse mouse strains and identified CC071 as the most susceptible strain. Importantly, this mouse strain has been shown by others to be also susceptible to several other RNA viruses. Through a combination of functional and genetic approaches in a cellular model, we identified a mutation in the Irf3 gene which plays a key role in activating the expression of interferon beta to induce the type I interferon response, the first line of host defense against the virus. This mutation fully explains the high viral replication observed in CC071 cells. However, it was not able to induce the elevated viremia and the disease signs displayed by CC071 ZIKV-infected mice, unraveling the implication of other host genes which are not associated with the type I interferon response. Because of the broad susceptibility of CC071 to multiple viruses, our results have implications beyond ZIKV infection and contribute to shedding light on the plurality of host mechanisms fighting infectious diseases.