AbstractThe large dsDNA virus HSV-1 is often considered to be genetically stable, however it is known to rapidly evolve in response to strong selective pressures such as antiviral drug treatment. Deep sequencing analysis has revealed that clinical and laboratory isolates of this virus exist as populations that contain a mixture of minor alleles or variants, similar to many RNA viruses. Classical virology methods often used plaque-purified virus populations to demonstrate consistent genetic inheritance of viral traits. Plaque purification represents a severe genetic bottleneck which may or may not be representative of natural transmission of HSV-1. Since HSV-1 has a low error rate polymerase but exhibits substantial genetic diversity, the virus likely uses other mechanisms to generate genetic diversity, including recombination, contraction and expansion of tandem repeats, and imprecise DNA repair mechanisms. We sought to study the evolution of HSV-1 in vitro, to examine the impact of this genetic diversity in evolution, in the setting of standard laboratory conditions for viral cell culture, and in the absence of strong selective pressures. We found that a mixed population of HSV-1 was more able to evolve and adapt in culture than a plaque-purified population, though this adaptation generally occurred in a minority of the viral population. We found that certain genetic variants appeared to be positively selected for rapid growth and spread in Vero cell culture, a phenotype which was also observed in clinical samples during their first passages in culture. In the case of a minor variant that induces a visually observable syncytial phenotype, we found that changes in minor variant frequency can have a large effect on the overall phenotype of a viral population.Author SummaryHerpes simplex virus type 1 (HSV-1) is a common virus, affecting over half of the adult human population, although it presents variable levels of disease burden and frequency of symptomatic recurrence. Antiviral treatments for HSV-1 infections are available, but thus far attempts at vaccine development have been foiled by insufficient immunity and/or viral escape. As a virus with a double-stranded DNA genome, HSV-1 is generally considered to be genetically stable and to have limited evolutionary potential. As these two statements are in conflict, we examined the ability of HSV-1 to evolve in a standardized cell culture setting. We utilized two HSV-1 isolates in this experiment, one with multiple viral genotypes present, which is similar to the viral populations seen in clinical settings, and one with a highly clonal viral population, which is similar to those often used in laboratory settings. After multiple rounds of replication, we analyzed the sequences of each passaged population. We found that the mixed viral population changed substantially over passage, and we were able to track specific genetic variants to phenotypic traits. By comparison, evolution in the clonal virus population was more limited. These data indicate that HSV-1 is capable of evolving rapidly, and that this evolution is facilitated by diversity in the viral population.
Distinguishing SARS-CoV-2 bonafide re-infection from pre-existing minor variant reactivation
