Defective interfering genomes during HSV-1 repeated infection

In many RNA and DNA viruses, undiluted passages of viruses in culture cells allow the formation of defective interfering genomes (DIGs). Undiluted passages show cyclic pattern of virus infectivity that is negatively correlated to the formation of DIGs. In RNA viruses DIG formation was associated also with immune modulation and viral persistence. In herpes simplex virus-1 (HSV-1, a large DNA virus) DIGs role is unknown although DIGs containing large deletions in their sequence were identified decades ago.

Previous experiments in our lab showed that different cell lines vary in the number of HSV-1 genomes that enter their nucleus and start expression and replication. Here we show that undiluted passaging of HSV-1 in different cell-lines results in changes in amplitude and frequency of the infectivity cyclic pattern (i.e. DIG formation). The frequency and amplitude are higher in cell lines that enable more genomes to start the replication. These findings were corroborated using qPCR. Sequencing of several of the undiluted passages suggests that each cell type generates different varieties of the DIG population and may affect the viral diversification rate.

Our results suggest that DIG formation frequency and amplitude in addition to the effective number of viral genomes initiating the replication effect the number of structural variations and thus viral evolution.