Characterization of a hepatitis C virus genotype 1 divergent isolate from an HIV-1 coinfected individual in Germany assigned to a new subtype 1o

Wang, Bo; Krüger, Luise; Machnowska, Patrycja; Eshetu, Amare; Gunsenheimer-Bartmeyer, Barbara; Bremer, Viviane; Hauser, Andrea; Bannert, Norbert; Bock, C.-Thomas

doi:10.1186/s12985-019-1135-7

Virology Journal

Table 1 Primers used for HCV quantification, genotyping and DE/17–0414 genome amplification

From: Characterization of a hepatitis C virus genotype 1 divergent isolate from an HIV-1 coinfected individual in Germany assigned to a new subtype 1o

Primer^a	Sequence (5′-3′)	Location^b	Reference
Real-time RT-PCR assay for HCV quantification
HCV-238_f	GAGGAACTACTGTCTTCACG	49–68	This study
HCV-239_r	TCGCAAGCACCCTATCAG	310–293
HCV-240_f	TCGCAAGCACCCTATCAG	76–94
HCV-235_r	AGTACCACAAGGCCTTTCG	290–272
Heminested RT-PCR assay for HCV genotyping
HCV-271_f	ACCACATCMRSTCCGTGTGG	7951–7970	This study
HCV-272_f	TCCGTGTGGRARGACYTSCTRGA	7962–7984
HCV-305_f	CTCCGTMTGGGAGGACTTGC	7961–7980
HCV-275_r	CTSGTCATAGCYTCCGTGAA	8635–8616
Heminested RT-PCR assays for DE/17–0414 genome amplification
HCV-235_r	AGTACCACAAGGCCTTTCG	290–272	This study
HCV-239_r	TCGCAAGCACCCTATCAG	310–293	This study
HCV-365_f	GGCGTTAGTATGAGTGTTGTGC	87–108	(Lu et al., 2014)
HCV-366_r	TCCCTGAAGAGTTGCGTATTCC	939–918
HCV-367_r	AGAAAGAGCAACCGGGAAGATT	864–843
HCV-368_f	TCTATCTTCCTTCTTGCCATCCTG	864–887
HCV-369_f	AGGGATTTACCATGTCACCAATGA	935–958
HCV-370_r	TCAAAGTCAGTAAGAGGTCGACAG	1747–1724
HCV-371_f	CCCGGTGCATGGTAGACTAC	2164–2183
HCV-372_r	CTCCACCCTCCGTTGGTTAG	3421–3492
HCV-373_r	CCGTTGGTTAGGGAGTCAGC	3412–3393
HCV-374_f	ACATTCTTGGCTACGTGCTGTA	3552–3573
HCV-375_f	CCCCATTATCCAGATGTACACCAA	3635–3658
HCV-387_r	TCTGGACTTCTCCCTCCACC	3531–3512	This study
HCV-388_f	GCCGCATCCAAACATTGAGG	4421–4440
HCV-389_f	CGGCAAAGCTATCCCCCTAG	4478–4497
HCV-390_r	CCCGCCTGTTTTGTCTGAGA	5089–5070
HCV-391_f	GCATCCAAAGAGGCTGAGGT	5565–5584
HCV-392_f	CATCCCTGCTGTCCCAACTT	5588–5607
HCV-393_r	TTATGTCAGCTCCGCATGGG	6456–6437
HCV-394_f	GACGCCGACCTCATAGAAGC	7017–7036
HCV-395_r	TGGCGTAACAAGGAGTTGCT	7708–7689
HCV-396_r	ATGGGCAGCTTGTTCTCCTC	7678–7659
HCV-360_f	CTCACCTGCTATCTCAAGGCAA	8487–8508
HCV-361_f	GTTATCTGTGAGAGTAGCGGGG	8574–8595

^aForward primer designation end with _f; reverse primer designations end with _r
^bNumbering is according to the HCV prototype strain of H77 (GenBank Acc. No. AF009606)

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ISSN: 1743-422X

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