CRISPR-Cas9 system-driven site-specific selection pressure on Herpes simplex virus genomes.

•CRISPR-Cas9 system provides selection pressure directly on the herpes simplex virus genome replication.•The specificity of the selection pressure provided by CRISPR-Cas9 system could identify single base-pair differences within mixed viral genomes.•Both Cas9 and Cas9 nickase (D10A) could perform the selection effect on the viral genome replication.•High viral m.o.i would promote the selection efficiency of the CRISPR-Cas9 system.•This method provides a tool for virus selection that would save labour and time.