Quantification of Pregenomic RNA and Covalently Closed Circular DNA in Hepatitis B Virus-Related Hepatocellular Carcinoma

Table 1

Sequences and positions of primers and probes used in this study.

Primer and probe	Region	Position	Polarity	Sequence (5′ to 3′)	Reference
Occult case determination
HBV 1	PreS-S	2815–2834	Sense	GGTCACCATATTCTTGGGAA	[6]
HBV 2	PreS-S	690–671	Antisense	AATGGCACTAGTAAACTGAG	[6]
HBV 17	PreS-S	3037–3057	Sense	AATCCAGATTGGGACTTCAA	[6]
HBV 4	PreS-S	459–440	Antisense	CCTTGATAGTCCAGAAGAAC	[6]
HBV 5	Precore-core	2021–2040	Sense	GCCTTAGAGTCTCCTGAGCA	[6]
HBV 6	Precore-core	2464–2448	Antisense	GTCCAAGGAATACTAAC	[6]
HBV 7	Precore-core	2048–2066	Sense	CCTCACCATACTGCACTCA	[6]
HBV 8	Precore-core	2385–2366	Antisense	GAGGGAGTTCTTCTTCTAGG	[6]
Pol 1 S	Polymerase	2412–2430	Sense	CGCGTCGCAGAAGATCTCA	[5]
Pol 1 AS	Polymerase	256–237	Antisense	CGAGTCTAGACTCTGTGGTA	[5]
Pol 2 S	Polymerase	2452–2476	Sense	GTATYCCTTGGACTCATAAGGTGGG	[5]
Pol 2 AS	Polymerase	2838–2814	Antisense	CTTGTTCCCAAGAATATGGTGACCC	[5]
X 1 S	X	1100–1121	Sense	CGCCAACTTACAAGGCCTTTCT	[5]
HBV 19	X	1550–1529	Antisense	CGTTCACGGTGGTCTCCAT	[6]
HBV 15	X	1380–1400	Sense	GCTAGGCTGTGCTGCCAACTG	[6]
HBV 21	X	1518–1497	Antisense	GGTCGGTCGGAACGGCAGACGG	[6]
Genotyping and amplification of “a” determinant region
HB2F	S	414–433	Sense	TGCTGCTATGCCTCATCTTC	[7]
HB2R	S	989–970	Antisense	CATACTTTCCAATCAATAGG	[7]
Amplification of core promoter and precore regions
HB7F	C	1611–1630	Sense	GAGACCACCGTGAACGCCCA	[7]
HB7R	C	2072–2048	Antisense	CCTGAGTGCTGTATGGTGAGG	[7]
cccDNA and pgRNA quantification
CCC	X/C	1555–1573	Sense	GTGCCTTCTCATCTGCCGG	[8]
PGP	X/C	1826–1843	Sense	CACCTCTGCCTAATCATC	[8]
BC1	X/C	1974–1955	Antisense	GGAAAGAAGTCAGAAGGCAA	[8]
hbvLC	C	1874–1848	Antisense	GGAGGCTTGAACAGTAGGACATGAAC	[8]
hbvFL	C	1897–1876	Antisense	CYAAAGCCACCCAAGGCACAGC	[8]