Kato H, Fujiwara K, Gish RG, Sakugawa H, Yoshizawa H, Sugauchi F, Orito E, Ueda R, Tanaka Y, Kato T, Miyakawa Y, Mizokami M. Classifying genotype F of hepatitis B virus into F1 and F2 subtypes. World J Gastroenterol 2005; 11(40): 6295-6304 [PMID: 16419158 DOI: 10.3748/wjg.v11.i40.6295]
Corresponding Author of This Article
Prof. Masashi Mizokami, Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan. mizokami@med.nagoya-cu.ac.jp
Article-Type of This Article
Viral Hepatitis
Open-Access Policy of This Article
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World J Gastroenterol. Oct 28, 2005; 11(40): 6295-6304 Published online Oct 28, 2005. doi: 10.3748/wjg.v11.i40.6295
Table 1 Demographic characteristics and liver diseases of the 11 patients from whom HBV isolates of genotype F were recovered
HBV strains
Accession number
Age (yr)
Gender
Ethnicity
Clinical diagnosis
USF10
AB059659
46
Female
Caucasian
Liver cirrhosis
USF1122
AB064315
46
Male
Hispanic
Liver cirrhosis
USF1778
AB059660
44
Male
Hispanic
Liver cirrhosis
USF2065
AB059661
47
Male
Hispanic
Acute hepatitis
USF2573
AB064316
67
Male
Hispanic
Liver cirrhosis
JPF1130
AB086397
43
Male
Asian
Chronic hepatitis
JPNTAKA
AB116654
NA
Male
Asian
NA
VENEZ2
AB116549
35
Male
Hispanic
Acute hepatitis
VENEZ4
AB116550
35
Male
Hispanic
Acute hepatitis
PANAM5
AB116551
NA
NA
NA
NA
PANAM6
AB116552
NA
NA
NA
NA
Table 2 Primers used for PCR and sequencing
Primer1
Polarity
Sequence (5’–3’)
Positions (nt)
HBV/Ff1
Sense
GGG TCA CCA TAT TCT TGG GAA
2 814–2 834
HBV/Fr1
Antisense
CGT TGC CGA GCA ACG GGG TAA AGG
1 163–1 140
HBV/Ff2
Sense
GTT TCT CCT GGC TCA GTT TA
660–679
HBV/Fr2
Antisense
AAA AAG TTG CAT GGT GCT GG
1 825–1 806
HBV/Ff3
Sense
ACG TCG CAT GGA GAC CAC CG
1 601–1 620
HBV/Fr3
Antisense
GAA CTG GAG CCA CCA GCA GG
75–56
HBV/Ff4
Sense
CCT CCT GCT TCC ACC AAT CG
3 124–3 143
HBV/Fr4
Antisense
AGA TGA GGC ATA GCA GCA GGA TG
431–409
HBV/Ff5
Sense
GTC TAG ACT CGT GGT GGA CTT CTC
246–269
HBV/Fr5
Antisense
AAG CCA GAC AGT GGG GGA AAG C
730–709
HBV/Ff6
Sense
CTC GCC AAC TTA CAA GGC CTT T
1 098–1 119
HBV/Fr6
Antisense
GAT TCA GCG CCG ACG GGA CGT A
1 447–1 426
HBV/Ff7
Sense
CTC TGC CGA TCC ATA CTG CGG AA
1 256–1 278
HBV/Fr7
Antisense
TGA GAT CTT CTG CGA CGC GGC
2 431–2 410
HBV/Ff8
Sense
TCA GGC AAG CTA TTT TGT GCT GG
2 064–2 086
HBV/Fr8
Antisense
TGT TCA CAT TTG TGT ATC AAA T
2 587–2 565
HBV/Ff9
Sense
GCC GCG TCG CAG AAG ATC TCA A
2 410–2 431
HBV/Fr9
Antisense
AAA ATG AGG CGC TAT GTG TGG ATT
2 811–2 788
Table 3 Sequence homology of seven HBV/F2 isolates among themselves and to seven HBV isolates representative of HBV/F1 as well as the other genotypes (A, B, C, D, E, and G)
Genomic regions
Homology within seven HBV/F2 isolates and that of HBV/F2 to seven representative of HBV/F1 as well as genotypes A, B, C, D, E, and G1
F2
F1
A
B
C
D
E
G
Full genome
97.5
91.6
86
85.9
85.7
85.7
86.1
84.5
(96.3–99.2)
(91.0–92.1)
(85.4–86.5)
(85.5–86.2)
(85.2–86.0)
(85.1–86.3)
(85.6–86.4)
(84.1–84.8)
PreS1 region
98.1
90
77.3
75.7
78.9
79.3
81.4
80.6
(97.2–99.4)
(89.1–90.5)
(76.8–78.2)
(75.1–76.5)
(77.9–80.1)
(78.3–80.2)
(80.7–82.0)
(80.4–81.1)
PreS2 region
97.4
90.9
82.9
79.2
82.6
81.2
83.3
81.3
(92.7–100)
(86.1–92.7)
(78.0–84.2)
(75.8–80.6)
(79.4–83.6)
(77.6–82.4)
(79.4–84.2)
(77.0–83.0)
S gene
99.4
96.4
92.2
92.6
91.3
92.7
92.6
92.8
(98.7–99.9)
(95.9–96.8)
(91.8–92.5)
(92.5–92.8)
(91.0–91.6)
(92.4–93.0)
(92.2–92.8)
(92.4–93.0)
C gene
95.8
91.9
84.8
87.3
86.6
84.9
85.8
87.2
(90.9–100)
(88.8–93.5)
(83.0–85.8)
(85.1–88.6)
(84.8–87.5)
(82.8–86.6)
(84.1–86.8)
(84.9–88.2)
P gene
97.9
91.7
86.2
85.8
86.3
86.1
86.5
86.1
(96.6–99.1)
(90.9–92.0)
(85.7–86.6)
(85.4–86.0)
(86.1–86.6)
(85.5–86.4)
(86.2–86.8)
(85.7–86.4)
X gene
97.1
91.1
87.7
88.7
85.4
89.2
88.3
84.2
(94.2–99.8)
(89.3–92.3)
(86.5–88.7)
(86.8–90.1)
(84.7–86.8)
(88.0–90.2)
(87.1–89.5)
(85.0–83.7)
Table 4 Homology in the entire nucleotide sequence of the seven HBV/F2 isolates to HBV/F1 isolates and among themselves
F2 subtype (this study)
F2 subtype (reported)
F1 subtype (this study)
USF10
USF1122
USF1778
USF2065
1853Nic
2928Nic
LAS2523
USF2573
JPF1130
JPNTAKA
PANAM5
PANAM6
VENEZ2
VENEZ4
HBV/F1 isolates
(reported)
AB036905
91.7
91.9
92.3
92.6
92.3
92.7
92.5
94.6
94.1
93.6
99.2
97.9
99
94.7
AB036910
91.7
91.9
92.3
92.7
92.2
92.6
92.6
94.7
94.1
93.6
99.2
98
99.5
94.8
AB036920
91.7
91.9
92.2
92.5
92.2
92.7
92.5
94.6
94
93.6
99.1
97.8
98.8
94.7
X69798
91.1
91.4
91.9
92.2
91.6
92.1
92.2
94.3
93.9
93.6
96.2
95.2
96.1
94.5
X75659
90.5
90.7
91.2
91.6
91
91.4
91.4
93.6
92.9
92.6
95.4
94.3
95.5
93.7
X75663
91
91.2
91.8
92.2
91.7
92.1
91.9
94
93.3
92.8
97.2
96
97.6
94.1
AY090455
91
91.1
91.5
91.9
91.4
91.9
91.9
94.2
93.8
93.4
96
94.9
95.8
94.3
AY090458
90.8
90.9
91.5
92
91.6
91.9
91.6
97.9
97.3
96.9
94.9
93.8
94.9
98.1
AY090459
90.8
90.8
91.5
91.9
91.6
91.9
91.5
98.2
97.5
97.2
95
93.9
94.9
98.3
AY090461
90.9
91
91.6
92
91.6
91.9
91.7
98.1
97.5
97.1
95
93.9
94.8
98.3
HBV/F1 isolates
(this study)
USF2573
91
91.1
91.6
92
91.8
92.1
91.8
–
98.5
97.9
94.8
93.7
94.7
99.6
JPF1130
90.7
90.6
91.3
91.5
91.3
91.6
91.3
98.5
–
97.8
94.3
93.4
94.2
98.4
JPNTAKA
90.5
90.5
91.1
91.3
91.0
91.3
91.1
97.9
97.8
–
93.9
92.9
93.7
97.9
PANAM5
91.9
92
92.4
92.8
92.3
92.8
92.7
94.8
94.3
93.9
–
98.6
99.2
95
PANAM6
91.1
91.2
91.7
91.7
91.4
91.9
91.7
93.7
93.4
92.9
98.6
–
98
93.8
VENEZ2
91.8
92.1
92.5
92.8
92.3
92.8
92.7
94.7
94.2
93.7
99.2
98
–
94.9
VENEZ4
91.1
91.2
91.7
92.1
91.9
92.2
92
99.6
98.4
97.9
95
93.8
94.9
–
F2 isolates
(this study)
USF10
–
97
96.9
97.2
96.3
96.6
97.9
91.0
90.7
90.5
91.9
91.1
91.8
91.1
USF1122
97
–
97.1
97.6
96.5
96.9
98.2
91.1
90.7
90.5
92
91.2
92.1
91.2
USF1778
96.9
97.1
–
98.6
97.2
97.4
98
91.6
91.3
91.1
92.4
91.7
92.5
91.7
USF2065
97.2
97.6
98.6
–
97.6
97.8
98.4
92
91.5
91.3
92.8
91.7
92.8
92.1
F2 isolates
(reported)
1853Nic
96.3
96.5
97.2
97.6
–
99.2
97.5
91.8
91.3
91.0
92.3
91.4
92.3
91.9
2928Nic
96.6
96.9
97.4
97.8
99.2
–
97.7
92.1
91.6
91.3
92.8
91.9
92.8
92.2
LAS2523
97.9
98.2
98
98.4
97.5
97.7
–
91.8
91.3
91.1
92.7
91.7
92.7
92
Table 5 Genotype- or subtype-specific nucleotides
HBV isolates
Nucleotide positions
Genotype
P gene
/subtype
22
1 467
1 552
1 754
2 495
2 558
2 579
2 596
2 603
2 606
2 622
2 628
2 634
2 636
2 660
3 121
3 129
X70185
A
T
G
T
T
G
T
T
T
C
T
A
A
A
A
T
A
T
D00329
B
–
–
–
–
–
–
–
–
A
C
–
–
–
–
–
G
–
D50520
C
–
–
–
–
A
–
–
A
–
–
–
–
–
–
–
G
–
D23681
D
–
–
–
–
–
A
C
–
–
A
–
–
C
–
–
G
G
X75657
E
–
–
–
–
–
–
–
–
T
–
–
–
–
C
–
G
G
AB056515
G
–
–
–
C
–
C
A
–
–
–
–
–
–
–
C
G
G
X68798
F1
–
–
–
–
–
–
–
–
–
A
T
–
–
–
–
G
G
X75658
F1
–
–
–
C
–
–
A
–
–
A
T
–
–
–
–
G
G
X75663
F1
–
–
–
C
–
–
A
–
–
G
T
–
–
–
–
G
G
AB036905
F1
–
–
–
C
–
–
A
–
–
G
T
–
–
–
–
G
G
AB036910
F1
–
–
–
C
–
–
A
–
–
G
T
–
–
–
–
G
G
AB036920
F1
–
–
–
C
–
–
A
–
–
G
T
–
–
–
–
G
G
USF2573
F1
–
–
–
–
–
–
A
–
G
–
T
–
–
–
–
G
G
JPF1130
F1
–
–
–
–
–
–
A
–
–
–
T
–
–
–
–
G
G
JPNTAKA
F1
–
–
–
–
–
–
A
–
–
–
T
–
–
–
–
G
G
PANAM5
F1
–
–
–
C
–
–
A
–
–
G
T
–
–
–
–
G
G
PANAM6
F1
–
–
–
C
–
–
A
–
–
G
T
–
–
–
–
G
G
VENEZ2
F1
–
–
–
C
–
–
A
–
–
G
T
–
–
–
–
G
G
VENEZ4
F1
–
–
–
T
A
–
A
–
–
–
T
–
–
–
–
G
G
USF10
F2
A
T
C
G
T
–
A
–
–
A
–
C
–
–
–
C
A
USF1122
F2
A
T
C
G
T
–
A
–
–
A
–
C
–
–
–
C
A
USF1778
F2
A
T
C
G
T
–
A
–
–
A
–
C
–
–
–
C
A
USF2065
F2
A
T
C
G
T
–
A
–
–
A
–
C
–
–
–
C
A
AY090454
F2
A
T
C
G
T
–
A
–
–
A
G
C
–
–
–
C
A
AY090457
F2
A
T
C
G
T
–
A
–
–
A
G
C
–
–
–
C
A
AY090460
F2
A
T
C
G
T
–
A
–
–
A
–
C
–
–
-
C
A
Citation: Kato H, Fujiwara K, Gish RG, Sakugawa H, Yoshizawa H, Sugauchi F, Orito E, Ueda R, Tanaka Y, Kato T, Miyakawa Y, Mizokami M. Classifying genotype F of hepatitis B virus into F1 and F2 subtypes. World J Gastroenterol 2005; 11(40): 6295-6304