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

Dengue viruses are mosquito-borne human pathogens whose global incidence in human infections is rising. Surveillance is hampered by the requirement for blood-based diagnostics. Interestingly, in several prior research studies, dengue virus nucleic acids and proteins could be detected in saliva, making saliva-based diagnostics a plausible alternative. However, the temporal relationships between exposure, viremia, salivary accumulation, and symptom onset remain poorly defined. To address this knowledge gap, nine participants were enrolled in clinical trial NCT04298138 to receive an inoculation with an attenuated dengue virus (DENV-3 strain CH53489). Matched blood and saliva specimens were collected over 10 days. 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. Strikingly, far more human genes showed increased transcript abundance exclusively in saliva (14%) than in PBMCs (5%) or both compartments simultaneously (6%), 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.IMPORTANCEDengue virus infections are detected using blood samples, either with nucleic acid amplification tests for the dengue virus genome (in the case of an active infection) or serology-based tests for antibodies recognizing dengue viruses (indicating a prior infection). The requirement for blood draws creates a barrier to dengue virus surveillance. Our data demonstrate that saliva can serve as an alternative biospecimen for detecting dengue virus genomes early in infection, with detection lagging blood by only 1.6 days-a modest and likely acceptable tradeoff given saliva's practical advantages. Unlike blood, saliva is non-invasive, self-collectible, requires no sharps, and is thermostable. We also identified host genes upregulated upon dengue infection, informing on the host response to infection. Our longitudinal study design enabled us to track the kinetics of transcript accumulation both by day post-infection and relative to symptom onset, providing high resolution into the host response to the virus.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT04298138.