Table 1.

Oligonucleotides used as primers in quantitative real-time PCR to detect viral immediate early (IE), late (L), or cellular (C) gene fragments. The orientations of the primers are indicated relative to the transcription unit (F for forward and R for reverse). PCR end points are defined relative to the transcription start site (+1) of each gene.

Gene	Class	Region	Oligonucleotide sequence	PCR endpoints
ICP0	IE	P	(F) 5′-GGCCGTGCATGCTAATGATA (R) 5′-CTTATACCCCACGCCTTTCC	−172 to −20
		ORF	(F) 5′-CTGTCGCCTTACGTGACCAA (R) 5′-CCATGTTTCCCGTCTGGTC	3022 to 3133
ICP4	IE	ORF	(F) 5′-GAAGTTGTGGACTGGGAAGG (R) 5′-GTTGCCGTTTATTGCGTCTT	4125 to 4257
ICP22	IE	ORF	(F) 5′-TTTGGGGAGTTTGACTGGAC (R) 5′-CAGACACTTGCGGTCTTCTG	1575 to 1712
ICP27	IE	P	(F) 5′-GTCCCGTTACCAAGACCAAC (R) 5′-GCACAGACAAGGACCAATCA	−235 to −102
		ORF	(F) 5′-TGCATCCTTCGTGTTTGTCATTCTGG (R) 5′-GCCGTCAACTCGCAGACACGACTC	1099 to 1249
ICP47*	IE	ORF	(F) 5′-GTACGACCATCACCCGAGTC (R) 5′-GACGGCACGCCTTTTAAGTA	808 to 935
VP16	L	P	(F) 5′-CAGCCCGCTCCGCTTCTCG (R) 5′-GCCGCCCCGTACCTCGTGAC	−272 to −47
U3	C	P	(F) 5′-GCACCACACCAGGAGCAAAC	−295 to −71
snRNA			(R) 5′-CGCTAGTTCCGATGCCATTAGG
18S	C		(F) 5′-CCGCAGCTAGGAATAATGGA	850 to 975
rRNA			(R) 5′-CGGTCCAAGAATTTCACCTC

^*The ICP47 primer overlaps with the US11 transcript. At early times of infections US11 is not expressed and thus this PCR detects ICP47 gene expression levels.