Figure 2.

Barriers and potential solutions for accurate quantification of host shutoff. The inefficient and asynchronous entry of EBV into lytic replication means that bulk populations of EBV infected cells are predominantly latently infected with decreasing levels of early and late lytic infection. As a consequence, detection of differentially expressed genes is diminished, especially mRNAs that are downregulated (or degraded) in lytic cells, such as those subject to host shutoff (compare bulk to actual). This limitation can be addressed via cell sorting approaches; however, given the marked differences in total mRNA in latent versus lytic cells, conventional normalization methods fail to accurately measure changes in gene expression. To account for such differences, exogenous spike-in RNAs can be added on a per cell basis. These (or similar) modifications are essential to capture host shutoff effects accurately on the cell gene expression. Figure created with BioRender.com.