Single cell immune profiling of dengue virus patients reveals intact immune responses to Zika virus with enrichment of innate immune signatures

Author summary Mosquitoes carry many globally important human pathogens including a family of related viruses: dengue virus, West Nile virus, Yellow Fever virus, and recently of critical significance, Zika virus. The Zika virus epidemic emerged very rapidly in the susceptible South American population and in many cases immune responses were unable to control the infection. Immune history is a key element of susceptibility or resistance to severe disease. We examined whether pre-existing infection would skew or divert immune resources and might play a role in the severity of Zika infection in the Americas. Using samples from dengue patients and healthy controls from India, we tested functional responses to Zika virus in the context of pre-existing dengue infection. We quantified frequency and functional status of 36 individual cell subsets in depth using advanced profiling techniques and a novel deep learning algorithm. We showed an intact response to new infection with Zika virus which was enriched for early innate immune pathways and robust even during existing dengue infection. Thus, our study suggests that concurrent dengue infection would not be expected to impair immune responses to new infection with Zika virus. The genus Flavivirus contains many mosquito-borne human pathogens of global epidemiological importance such as dengue virus, West Nile virus, and Zika virus, which has recently emerged at epidemic levels. Infections with these viruses result in divergent clinical outcomes ranging from asymptomatic to fatal. Myriad factors influence infection severity including exposure, immune status and pathogen/host genetics. Furthermore, pre-existing infection may skew immune pathways or divert immune resources. We profiled immune cells from dengue virus-infected individuals by multiparameter mass cytometry (CyTOF) to define functional status. Elevations in IFN beta were noted in acute patients across the majority of cell types and were statistically elevated in 31 of 36 cell subsets. We quantified response to in vitro (re)infection with dengue or Zika viruses and detected a striking pattern of upregulation of responses to Zika infection by innate cell types which was not noted in response to dengue virus. Significance was discovered by statistical analysis as well as a neural network-based clustering approach which identified unusual cell subsets overlooked by conventional manual gating. Of public health importance, patient cells showed significant enrichment of innate cell responses to Zika virus indicating an intact and robust anti-Zika response despite the concurrent dengue infection.