Epstein-Barr virus reactivation induces divergent abortive, reprogrammed, and host shutoff states by lytic progression
Viral infection leads to heterogeneous cellular outcomes ranging from resistance to virion amplification and cell death. In this study, we apply single-cell techniques to analyze diverse fate trajectories during Epstein-Barr virus (EBV) lytic reactivation in three B cell models. We expand upon the previous finding that c-Myc regulates lytic reactivation and determine that MYC downregulation during the lytic phase is correlated with a loss of germinal center (GC) B cell expression signatures. Consistent with prior work, lytic induction yields both abortive and complete reactivation. Abortive lytic cells, which express high STAT3 and initiate but do not complete the lytic cycle, also upregulate NF-kB and IRF3 pathway target genes. Cells that proceeded through the full lytic cycle exhibited unexpected and striking expression of genes associated with cellular reprogramming, developmental progenitor phenotypes, and cytokine upregulation. Distinct subpopulations of lytic cells further displayed variable profiles for transcripts known to escape virus-mediated host shutoff. These data reveal previously unknown and promiscuous outcomes of lytic reactivation with broad implications for viral replication and EBV-associated oncogenesis. Overall design: Induction of EBV lytic reactivation in three B cell model systems was examined using scRNA-seq. The models used in this study included two Burkitt Lymphoma cell lines (Akata, P3HR1-ZHT), one of which (P3HR1-ZHT) is engineered for chemically-inducible viral reactivation, and one lymphoblastoid cell line (B958-ZHT) also engineered for inducible reactivation with 4-hydroxytamoxifen (HT). Sequence libraries were prepared from P3HR1-ZHT cells under the following conditions: unstimuated (UT), methanol control treatment for 24 h (MeOH), 24 h after treatment with HT (HT_24h; 2 replicates), 48 h after HT (HT_48h), and 72 h after HT (HT_72h). Sequence libraries from B958-ZHT cells were prepared from the following conditions: unstimulated (UT) and 24 h after HT (HT_24h). Sequence libraries from Akata cells were prepared from the following conditions: unstrimulated (UT) and 24 h after lytic induction with anti-Ig antibody (Ig).