Article Figures & Data
Figures
- FIG. 1.
Neighbor-joining trees for NS5B sequences (340 bp) (positions 8276 to 8615) and C/E1 sequences (424 bp) (positions 869 to 1292). Phylogenies for genotype 1 NS5B (a), genotype 2 NS5B (b), genotype 3 C/E1 (c), genotype 4 C/E1 (d), and genotype 6 NS5B (e) sequences are shown. The phylogenetic tree for genotype 1 sequences was rooted using genotype 4a sequence ED43 as the outgroup, while the phylogenetic trees for sequences of genotypes 2, 3, 4, and 6 were rooted using genotype 1a sequence HCV-1 as the outgroup. The numbers at the nodes represent the percent bootstrap support for 1,000 replicates. Only values over 75% are shown. Bars at the base of the trees show the genetic divergence. Letters following isolate names indicate countries of origin of patients: BI, Burundi; CA, Canada; CD, Democratic Republic of Congo; CG, Congo; CI, Côte d'Ivoire; CM, Cameroon; DO, Dominican Republic; HT, Haiti; IN, India; IS, Indian subcontinent; IT, Italy; KH, Cambodia; LA, Laos; LB, Lebanon; MA, Morocco; PA, Pakistan; RW, Rwanda; VN, Vietnam.
- FIG. 2.
Unrooted neighbor-joining tree of NS5B sequences (340 bp) (positions 8276 to 8615) showing the relationship of QC69 and QC272 to representatives of genotypes 1 to 6, CS101285, and CS101300 sequences. The bar at the base of the tree shows the genetic divergence.
- FIG. 3.
Comparison of sequences in the 5′UTR region (196 bp) (positions 96 to 291). (a) Comparison of QC69, QC272, genotype 6a QC169 and QC242, and genotype 6 QC148 sequences to HCJ6 (genotype 2a) and EUHK2 (genotype 6a) sequences. Nucleotides different from those of genotype 1a HCV-1 are indicated. (b) Thirty-seven genotype 6 sequence profiles obtained for 100 non-6a, non-6b variants. Nucleotides different from those of genotype 1b HCV-BK are indicated.
Tables
- TABLE 1.
Primers used for viral genome detection and sequencing
Genomic region and primer Polarity Sequence Positiona Size of PCR product (bp) NS5B DM100 Antisense 5′-TACCTVGTCATAGCCTCCGTGAA-3′ 8616-8638 389 DM101 Sense 5′-TTCTCRTATGAYACCCGCTGYTTTGA-3′ 8250-8275 DM106 Antisense 5′-GGNGCYGAGTAYCTGGTCATGGC-3′ 8625-8647 407 DM107 Sense 5′-CCHATGGGGTTYTCCTAYGACACCAG-3′ 8241-8266 DM104 Antisense 5′-TAYCTGGTCATAGCNTCCGTAAA-3′ 8616-8638 389 DM105 Sense 5′-TTCTCCTAYGACACCAGRTGYTTTGA-3′ 8250-8275 DM87 Antisense 5′-CATAGCCTCCGTGAAGGCTCTC-3′ 8609-8630 DM88 Antisense 5′-CATAGCCTCCGTGAAGACTCGT-3′ 8609-8630 DM113 Sense 5′-GAYACCCGCTGYTTGACTC-3′ 8259-8378 DM128 Sense 5′-TGAGGAGTCCATATACCAGGC-3′ 8306-8326 DM129 Sense 5′-TGAGGAGTCAATCTACCAATG-3′ 8306-8326 DM130 Sense 5′-ACTGAGAGCGAYATCCGTACG-3′ 8286-8306 DM131 Sense 5′-ACTGAGARTGACATCCGTGTT-3′ 8286-8306 DM132 Antisense 5′-GCCGCATACCAGCATTGTGGG-3′ 8532-8552 DM133 Antisense 5′-TCCACACACCAGCATAACGGG-3′ 8532-8552 DM134 Antisense 5′-CGTGAAGGCTCGCAGGCTCGC-3′ 8601-8621 DM136 Antisense 5′-CTGGACCCCTGCACTTTCACA-3′ 8571-8591 DM137 Sense 5′-AATGTTGTGACCTGGACCCCC-3′ 8323-8343 DM138 Antisense 5′-ATCGACGCCATCACTCTCAGC-3′ 8571-8591 DM139 Sense 5′-AATGTTGTAATCTTGAGCCGG-3′ 8323-8343 C/E1 DM108 Antisense 5′-TTCATCATCATRTCCCANGCCAT-3′ 1293-1315 473 DM109 Sense 5′-AAYYTDCCCGGTTGCTCTTTYTCTAT-3′ 843-868 DM110 Antisense 5′-GTRGGNGACCARTTCATCATCA-3′ 1306-1327 494 DM111 Sense 5′-GCAACAGGGAAYYTDCCYGGTTGCTC-3′ 834-859 5′UTR DM50 Antisense 5′-CTCGCAAGCACCCTATCAGG-3′ 292-311 241 DM51 Sense 5′-GAAAGCGTCTAGCCATGGCGTTAGT-3′ 71-95 ↵ a Relative to H77 (GenBank accession number AF009606).
- TABLE 2.
Prevalence of HCV genotypes for 8,237 patients determined by sequence analysis of the NS5B region
Subtype Prevalence for genotype: 1 2 3 4 5 6 NGa No. % No. % No. % No. % No. % No. % No. % Total 4,889 59.4 741 9.00 2113 25.7 293 3.56 53 0.64 146 1.77 2 0.02 a 3,748 76.7 236 31.8 2095 99.1 115 39.2 53 100 30 20.5 b 1,105 22.6 353 47.6 7 0.33 1 0.34 0 c 2 0.04 81 10.9 0 10 3.41 0 d 6 0.12 1 0.13 0 34 11.6 0 e 2 0.04 1 0.13 0 1 0.34 59 40.4 f 0 0 0 2 0.68 1 0.68 g 5 0.10 0 2 0.09 1 0.34 0 h 2 0.04 0 1 0.05 6 2.05 2 1.37 i 2 0.04 30 4.05 7 0.28 0 0 j 2 0.04 4 0.54 0 0 k 4 0.08 6 0.81 1 0.05 45 15.4 0 l 0 0 13 4.44 2 1.37 m 4 0.54 5 1.71 0 n 0 4 1.37 0 o 0 4 1.37 10 6.85 p 0 1 0.34 7 4.79 q 0 6 2.05 6 4.11 r 4 0.54 30 10.2 8 5.48 s 3 2.05 t 2 0.68 UCb 11 0.22 21 2.83 1 0.05 13 4.44 18 12.3 - TABLE 3.
Sex ratio and mean age values of patients among the various HCV genotypes
Genotype No. of patients Sex ratioa Age (yr) (mean ± SD) All patients Men Women All 8,237 2.2 44.3 ± 11.4 44.0 ± 10.3 45.0 ± 13.7 1 all 4,889 2.4 44.3 ± 11.0 44.1 ± 9.9 44.8 ± 13.4 1a 3,748 2.7 42.4 ± 9.5 42.9 ± 8.8 41.1 ± 11.2 1b 1,105 1.6 50.7 ± 13.0 49.2 ± 12.1 53.0 ± 14.1 2 all 741 1.5 50.4 ± 13.2 48.6 ± 11.9 53.2 ± 14.4 2a 236 1.1 52.8 ± 13.1 49.0 ± 11.4 57.0 ± 13.6 2b 353 2.4 44.5 ± 10.4 44.3 ± 9.4 44.8 ± 12.4 2c 81 1.1 62.4 ± 10.6 63.4 ± 9.5 61.3 ± 11.7 2i 30 1.5 60.3 ± 13.1 58.4 ± 11.7 63.1 ± 14.4 3 all 2,113 2.7 40.6 ± 9.5 41.3 ± 9.1 38.7 ± 10.3 3a 2,095 2.7 40.5 ± 9.5 41.2 ± 9.1 38.7 ± 10.3 4 all 293 1.3 49.2 ± 12.5 48.4 ± 11.8 50.2 ± 13.2 4a 115 2.8 50.8 ± 12.9 49.1 ± 12.1 55.6 ± 14.1 4d 34 1.6 42.5 ± 8.9 42.8 ± 8.8 42.1 ± 9.1 4k 45 1.0 49.8 ± 13.7 50.2 ± 12.0 49.4 ± 15.1 4r 30 0.5 50.6 ± 10.3 52.1 ± 12.0 49.9 ± 9.3 5 all (5a) 53 0.7 60.4 ± 13.7 60.8 ± 16.0 60.1 ± 11.9 6 all 146 1.5 51.9 ± 10.8 51.1 ± 10.1 53.1 ± 11.8 6a 30 2.0 47.3 ± 12.3 46.9 ± 12.1 48.1 ± 12.5 6e 59 1.1 53.3 ± 10.3 50.5 ± 9.4 56.5 ± 10.3 ↵ a Male-to-female ratio.
- TABLE 4.
Frequency of 5′UTR sequence profiles observed for genotype 6 subtypes other than subtypes 6a and 6b
Profile(s) No. with subtype: Total no. of observations 6c 6e 6f 6h 6l 6o 6p 6q 6r 6s 6 1 28 6 34 2 10 1 1 12 3 4 1 2 7 4 7 7 5 1 1 6-8 3 3 9 3 1 4 10 3 3 11 and 12 2 2 13 2 2 14-18 5 5 19 1 1 20 1 1 2 21-25 5 5 26 1 1 27 1 1 28 1 1 29-37 9 9 Total no. of sequence profiles 1 9 1 2 2 1 3 6 2 3 14
