Acute hepatitis C in a chronically HIV-infected patient: Evolution of different viral genomic regions

Table 1 Oligonucleotide primers used to amplify various HIV and HCV regions

Viral region	Nucleotide position	Primer sequence (5'→3')	PCR cycling parameters
HIV			5 min at 94 °C, 40 cycles of
gag			30 s at 94°C, 30 s at 55°C and
OS	4653-4675	CCCTACAATCCCCAAAGTCAAGG	45 s at 72°C and a final
OA	4956-4976	TACTGCCCCTTCACCTTTCCA	extension of 7 min at 72 °C
V3 loop
OS	6957 - 6976	GTACAATGTACACATGGAAT
OA	7357 - 7376	GTAGAAAAATTCCCCTCCAC	Idem HIV-gag PCR
IS	7010 - 7029	TGGCAGTCTAGCAGAAGAAG
IA	7319 - 7339	ACAATTTCTGGGTCCCCTCCT
HCV
5UT
OS	44 - 69	CCTGTGAGGAACTACTGTCTTCACGC	Idem HIV-gag PCR
OA	321 - 341	GGTGCACGGTCTACGAGACCT
HVR1
OS	1273-1296	GCCATATAACGGGTCACCGCATGG
OA	1681-1704	TCTCAGGACAGCCTGAAGMGTTGA	Idem HIV-gag PCR
IS	1296-1379	GCATGGGATATGATGATGAACTGG
IA	1623-1646	GGTGTTGAGGCTATCATTGCARTT
core			5 min at 94 °C, 30 cycles of
OS	272 - 291	CGAAAGGCCTTGTGGTACTG	1 min at 94 °C, 1 min at 50 °C
OA	1020 - 1037	CTCGCGRACGCAAGGGAC	and 2 min at 72 °C and a final
IS	281 - 302	TTGTGGTACTGCCTGATAGGGT	extension of 10 min at 72 °C
IA	956 - 976	ATACTCGAGTTAGGGCAATCA
NS5A
OS	6716 - 6739	TAGATGGGGTGCGCCTGCAYAGGTT
OA	7310 - 7332	GCTTCTTCCGRGGCGGAGGCACWG	Idem HCV core PCR
IS	6734-6753	TAGGTTTGCGCCCCCCTGMA
IA	7287-7306	GGGGACYKTGGAGGTGGAAG

Notes: OS: outer sense primer; OA: outer antisense; IS: inner sense; IA: inner antisense. Nucleotide positions were according to HIVHXB2 (K03455) for the HIV region and to HCV-1 (M62321) for HCV regions. Degenerate bases were indicated with standard codes of the International Union of Pure and Applied Chemistry.