Longitudinal single-cell RNA-sequencing (scRNAseq) of broncho-alaveolar compartment of rhesus macaque model of COVID-19

To gain insights into the early immune dynamics of transcriptional changes during SARS-CoV-2 infection in airways, we performed longitudinal scRNA-Seq of the broncho-alveolar lavage (BAL) cells isolated from SARS-CoV-2 infected rhesus macaques. We found early induction of innate type-1 interferon responses with accumulation of a distinct macrophage population that possesses an interferon-driven innate anti-viral gene signature early during infection. Overall design: BAL cells isolated from young rhesus macaques infected with SARS-CoV-2 WA1 strain at longitudinal timepoints representing pre-infection, acute and post-acute phases of COVID-19 were cryopreserved and analyzed by scRNAseq to reveal early innate immune dynamics.