The Homepage of Dr. Edward K. Wagner 
border corner

Herpes simplex virus Research

The HSV Genome

The HSV-1 genome is a linear, double stranded DNA duplex 152,000 base pairs in length, and with a base composition of 67% G + C. The genome circularizes upon infection. Because the genome circularizes, the transcription and genetic map is conveniently shown as a circle.

electron microscope image of HSV genome
Click image for closer view.

hsv genome map
Click image for closer view.

Since the virus encodes nearly 100 transcripts and more than 70 open translational reading frames (ORFs), the map is complex. Still, lack of splicing of HSV transcripts means that most ORFs are expressed by a single transcript.


The HSV genome can be divided
into six important regions

1 The ends of the linear molecules-the "a" sequences. These are important in both circularization of the viral DNA, and in packaging the DNA in the virion.

2 The 9,000 bp long repeat (RL), which encode both an important immediate early regulatory protein (a0) and the promoter of and most of the "gene" for the latency associated transcript (LAT).

3 The long unique region (UL), which is 108,000 bp long, encodes at least 56 distinct proteins (actually more because some ORFs are spliced and expressed in redundant ways). It contains genes for the DNA replication enzymes and the capsid proteins, as well as many other proteins.

4 The 6,600 bp short repeats (RS) encode the very important a immediate early protein. This is a very powerful transcriptional activator. It acts along with a0 and a27 (in the UL) to stimulate the infected cell for all viral gene expression that leads to viral DNA replication.

5 The origins of replication. The oriL is in the middle of the UL region. The oriS is in the RS and thus, is present in two copies. All sets of ori's operate during infection to give a very complicated replication complex--very similar to that seen in the replication of phage T4.

6 The 13,000 bp unique short region (US) encodes 12 ORFs, a number of which are glycoproteins important in viral host range and response to host defense.