Longitudinal analysis of viral and host RNA in blood and saliva during controlled human dengue virus 3 infections

Dengue virus genomes could be detected by RT-qPCR in both blood and saliva before the onset of symptoms in most individuals. The earliest time of detection in blood and saliva was 3.4 and 5.0 days post infection, respectively. Using this sample set, we also measured host transcriptional responses to dengue infection in both biospecimens from two participants using RNA sequencing.

Strikingly, far more human genes showed increased transcript abundance exclusively in PBMCs (4%) or saliva (15%) than in both compartments simultaneously (5%), revealing compartment-specific host responses. For 21 of the human transcripts that increased in response to dengue infection, we quantified their daily abundance across the course of DENV-3 infection in all study participants. Together, these findings demonstrate that sensitive dengue virus detection in saliva should be possible and establish that both blood and saliva capture early host responses to infection.