RNA-Sequencing of Saliva Samples from COVID-Infected and Vaccinated Subjects

SARS-CoV-2 virus is known to infect the oral cavity and can be readily detected using PCR-based testing. In this study, we examined the host transcriptomic response to PCR-confirmed SARS-CoV-2 virus infection, vaccination against SARS-CoV-2, or breakthrough infection following vaccination using RNA-sequencing. The identification of the viral variant for all samples was obtained using full viral genome sequencing. Approximately equal numbers of males and females were used for every major variant lineage. Results indicate strong anti-viral responses in each case, with some differences due to variant strain and vaccination history, as well as age and sex. Overall design: Human subjects participating in COVID-19 surveillance testing provided consent and submitted a saliva sample using a swab-based collection device. PCR testing was performed and SARS-CoV-2 genome sequencing completed on all positive subjects. Vaccine histories were also obtained. RNA was purified and used to create strand-specific libraries for next generation sequencing (RNA-Seq) with single-end reads. Resulting reads were mapped and quantified at the transcript level using Salmon, and filtered to remove features with less than 1 observed count in fewer than 80% of the samples. Normalization was applied using TPM + 1, followed by quantile normalization and log2 transformation.