Gene Expression Correlates with the Number of Herpes Viral Genomes Initiating Infection in Single Cells

Abstract

Viral gene expression varies significantly among genetically identical cells. The sources of these variations are not well understood and have been suggested to involve both deterministic host differences and stochastic viral host interactions. For herpesviruses, only a limited number of incoming viral genomes initiate expression and replication in each infected cell. To elucidate the effect of this limited number of productively infecting genomes on viral gene expression in single cells, we constructed a set of fluorescence-expressing genetically tagged herpes recombinants. The number of different barcodes originating from a single cell is a good representative of the number of incoming viral genomes replicating (NOIVGR) in that cell. We identified a positive correlation between the NOIVGR and viral gene expression, as measured by the fluorescent protein expressed from the viral genome. This correlation was identified in three distinct cell-types, although the average NOIVGR per cell differed among these cell-types. Among clonal single cells, high housekeeping gene expression levels are not supportive of high viral gene expression, suggesting specific host determinants effecting viral infection. We developed a model to predict NOIVGR from cellular parameters, which supports the notion that viral gene expression is tightly linked to the NOIVGR in single-cells. Our results support the hypothesis that the stochastic nature of viral infection and host cell determinants contribute together to the variability observed among infected cells.

Single-Cell Analysis Uncovers a Vast Diversity in Intracellular Viral Defective Interfering RNA Content Affecting the Large Cell-to-Cell Heterogeneity in Influenza A Virus Replication

“…Conversely, we found that the fraction of host cell mRNAs was decreased in high-yield cells. This was similarly observed for herpes virus-infected single cells [63]. Here, a higher cellular gene expression coincided with lower viral gene expression.…”

Spatiotemporal dynamics of HSV genome nuclear entry and compaction state transitions using bioorthogonal chemistry and super-resolution microscopy

“…Thus while there is a distinct genome decompaction after nuclear import, this is constrained in a relatively regular manner. The distribution of the numbers of genomes appearing in the nucleus and the relationship to moi bear similarity to those from physical analysis of adenovirus genome entry [16] and are relevant also to conclusions from other studies on the numbers of herpesvirus nuclear genomes that participate in transcription and replication [61][62][63]. We observed that at a standard moi of 10 pfu/cell (100-200 particles coating a cell), although a small percentage of nuclei could contain relatively high numbers, the mean numbers of nuclear genome foci was approximately 5 and around 90% of cells had fewer than 10.…”

HSV-1 single cell analysis reveals anti-viral and developmental programs activation in distinct sub-populations

“…A later study measured the burst size from individual HeLa cells infected 32 with Herpes Simplex virus 1 (HSV-1) and found that many of the infected cells did not release any progeny, 33 that the variability between individual cells was high and that it did not correlate with the multiplicity of 34 infection (MOI) used (Wildy et al, 1959). More One well-known source of this variability is the random distribution of the number of viruses that individual 39 cells encounter (Parker, 1938;Smith, 1968;Cohen and Kobiler, 2016). Another source is genetic variability 40 in the virus population, with some virus particles being unable or less fit to establish infection (Huang and 41 Baltimore, 1970; Lauring et al, 2013;Stern et al, 2014).…”