Characteristics of Hepatitis B Virus Genotype and Sub-Genotype in Hepatocellular Cancer Patients in Vietnam
Abstract
:1. Introduction
2. Materials and Methods
2.1. DNA Extraction, Nested PCR, and Complete Genome Sequencing
2.2. HCV RNA Detection
2.3. Phylogenetic Analysis
2.4. Mutational Analysis
2.5. Statistical Analysis
3. Results
3.1. Phylogenetic Analysis of HBV Genotype
3.2. Distribution of Age and Gender Factors by Genotypes
3.3. Mutational Regions of HBV Genotypes B and C
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
HBV | Hepatitis B Virus |
WHO | World Health Organization |
HCC | Hepatocellular Carcinoma |
RFLP | Restriction Fragment Length Polymorphism reaction |
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Region | Nucleotide | Amino Acid | Genotype B n= 62 | Genotype C n = 45 | p Value | |
---|---|---|---|---|---|---|
PreS1 (2848–3204) | A2962G | N38E | 60 (96.8) | 0 | <0.001 * | |
C2964A | N38E | 60 (96.8) | 0 | <0.001 * | ||
C3026A | A60V | 61 (98.4) | 44 (97.8) | 0.818 * | ||
C3116T | A90V | 2 (3.2) | 1 (2.2) | 0.756 * | ||
PreS2 (3205–155) | A3205G | M1V (Stop) | 5 (8.1) | 2 (4.4) | 0.696 * | |
A3205C | M1L (Stop) | 1 (1.6) | 0 | 1.000 * | ||
T3206C | M1T | 0 | 3 (6.7) | 0.071 * | ||
T31C | No change | 1 (1.6) | 0 | 1.000 * | ||
T53C | F22I | 9 (14.5) | 11 (24.4) | 0.193 ** | ||
S (155–835) | A162G | N3S | 1 (1.6) | 45 (100) | <0.001 * | |
C512T | P120S | 2 (3.2) | 0 | 0.508 * | ||
C512A | P120T | 5 (8.1) | 0 | 0.072 * | ||
C531T | T126I | 0 | 25 (55.6) | <0.001 * | ||
C531A | T126N | 0 | 2 (4.4) | 0.175 * | ||
A551T | M133L | 5 (8.1) | 0 | 0.072 * | ||
T552C | M133T | 0 | 1 (2.2) | 0.421 * | ||
G587A | G145R | 0 | 1 (2.2) | 0.421 * | ||
G588C | G145A | 0 | 2 (4.4) | 0.175 * | ||
T705C | V184A | 3 (4.8) | 1 (2.2) | 0.637 * | ||
T766A | S204R | 11 (17.7) | 0 | 0.002 * | ||
X (1374–1838) Enhancer II (1685–1773) | G1613A | NC | 23 (37.1) | 16 (35.6) | 0.870 ** | |
C1653T | H94Y | 8 (12.9) | 6 (13.3) | 0.948 ** | ||
G1721A | No change | 3 (4.8) | 39 (86.7) | <0.001 ** | ||
X (1374–1838) BCP (1751–1769) | A1762T | K130M | 32 (51.6) | 43 (95.6) | 0.000 * | |
G1764A | V131I | 31 (50) | 43 (95.6) | 0.000 * | ||
G1764C | 0 | 1 (2.2) | 0.421 * | |||
A1762T + G1764A | 31 (50) | 42 (93.3) | <0.001 * | |||
C1766T + (G1764A) | V131I | 6 (9.9) | 3 (6.7) | 0.731 * | ||
C1766T | No chance | 1 (1.6) | 0 | 1.000 * | ||
T1768A | F132Y | 8 (12.9) | 4 (8.9) | 0.758 * | ||
A1775G | No change | 1 (1.6) | 24 (53.3) | 0 * | ||
Precore (1814–1900) | T1858C | No change | 1 (1.6) | 41 (91.1) | <0.001 * | |
G1896A | W28Stop | 46 (74.2) | 2 (4.4) | <0.001 * | ||
G1899A | G29D | 6 (9.7) | 4 (8.9) | 1.000 * | ||
Core region (1901–2452) | C2002T | No change | 1 (1.6) | 1 (2.2) | 1.000 * | |
A2149T/C | E83D | 5 (8.1) | 3 (6.7) | 1.000 * | ||
A2159G | 11 (17.7) | 6 (13.3) | 0.538 ** | |||
A2189T | I97F | 2 (3.2) | 1 (2.2) | 1.000 * | ||
A2189C–C2191T | ||||||
A2189C | I97L | 19 (30.6) | 15 (33.3) | 0.768 ** | ||
A2189T-C2191T | ||||||
C2198A | L100I | 15 (24.2) | 10 (22.2) | 0.812 ** | ||
G2203A | No change | 1 (1.6) | 0 | 1.000 * | ||
Polymerase (2307–1623) | Putative Nar mutation | G287A | S53N | 47 (75.8) | 0 | <0.001 * |
A286G-G287A | S53D | 7 (11.3) | 0 | 0.021 * | ||
T382G | S85A | 0 | 1 (2.2) | 0.421 * | ||
A400C | I91L | 56 (90.3) | 40 (88.9) | 0.810 ** | ||
A400C-T402G | ||||||
C505T | H126Y | 1 (1.6) | 0 | 1.000 * | ||
C512A | T128N | 5 (8.1) | 0 | 0.072 * | ||
C512T | T128I | 1 (1.6) | 0 | 1.000 * | ||
A511G | T128A | 0 | 1 (2.2) | 0.421 * | ||
A544C | N139H | 1 (1.6) | 0 | 1.000 * | ||
A544C-C546A | N139Q | 1 (1.6) | 0 | 1.000 * | ||
A544G-C546A | N139E | 0 | 1 (2.2) | 0.421 * | ||
G587A | R153Q | 0 | 2 (4.4) | 0.175 * | ||
G700A | V191I | 0 | 1 (2.2) | 0.421 * | ||
G748A | V207M | 11 (17.7) | 0 | 0.002 * | ||
G748C | V207L | 0 | 1 (2.2) | 0.421 * | ||
T766A | S213T | 10 (16.1) | 0 | 0.005 * | ||
A774C | Q215H | 2 (3.2) | 0 | 0.508 * | ||
T779G | L217R | 1 (1.6) | 0 | 1.000 * | ||
A/G783C | E218D | 2 (3.2) | 0 | 0.508 * | ||
T791A | F221Y | 59 (95.2) | 5 (11.1) | <0.001 * | ||
T790C-T791A | F221H | 1 (1.6) | 0 | 1.000 * | ||
T814A | L229M | 2 (3.2) | 0 | 0.508 * | ||
T814G | L229V | 1 (1.6) | 0 | 1.000 * | ||
T815G | L229W | 0 | 1 (2.2) | 0.421 * | ||
A826G | I233V | 2 (3.2) | 0 | 0.508 * | ||
A841C-T843C | N238H | 62 (100) | 0 | <0.001 * | ||
A841C-A842C | ||||||
A842C | N238T | 0 | 11 (24.4) | <0.001 * | ||
A841G-A842C | N238A | 0 | 3 (6.7) | 0.071 * | ||
A895G | S256G | 12 (19.4) | 0 | 0.001 * | ||
A895G-G896C | S256A | 4 (6.5) | 0 | 0.137 * | ||
Pretreatment mutation | A241G | T38A | 0 | 1 (2.2) | 0.421 * | |
C242A | T38K | 0 | 1 (2.2) | 0.421 * | ||
T499C | Y124H | 61 (98.4) | 4 (8.9) | <0.001 * | ||
T499A | Y124N | 1 (1.6) | 0 | 1.000 * | ||
T499G | Y124D | 0 | 1 (2.2) | 0.421 * | ||
C/T531G | D134E | 0 | 3 (6.7) | 0.071 * | ||
G529A-A530G | D134S | 0 | 1 (2.2) | 0.421 * | ||
G529A | D134N | 1 (1.6) | 1 (2.2) | 0.818 * | ||
A544C-C546A | N139Q | 1 (1.6) | 0 | 1.000 * | ||
A544G-C546A | N139E | 0 | 1 (2.2) | 0.421 * | ||
A544C | N139H | 2 (3.2) | 0 | 0.508 * | ||
A799G | I224V | 61 (98.4) | 28 (62.2) | <0.001 * |
Total n (%) | Genotype B n (%) | Genotype C n (%) | |
---|---|---|---|
107 (100%) | 62 (57.9%) | 45 (42.1%) | |
Subgenotype | |||
B4 | 62 (57.9%) | ||
C1 | 45 (42.1%) | ||
Age (Mean ± SD) | 51.4 ± 11.4 | 52.9 ± 11.9 | 49.4 ± 10.4 |
30 | 1 (0.9%) | 1 (1.6%) | 0 |
31–40 | 20 (18.7%) | 9 (14.5%) | 11 (24.4%) |
41–50 | 35 (32.7%) | 20 (32.3%) | 15 (33.3%) |
51–60 | 27 (25.2%) | 15 (24.2%) | 12 (26.7%) |
61–70 | 17 (15.9%) | 12 (19.4%) | 5 (11.1%) |
71–80 | 7 (6.5%) | 5 (8.1%) | 2 (4.4%) |
Gender | |||
Male | 94 (87.9%) | 55 (88.7%) | 39 (86.7%) |
Female | 13 (12.2%) | 7 (11.3%) | 6 (13.3%) |
Biochemistry (Mean ± SD) | |||
ALT (U/L) | 56.8 ± 47.6 | 45.2 ± 39.3 | 72.9 ± 53.4 |
AST (U/L) | 61.9 ± 40.4 | 61.1 ± 46.1 | 62.9 ± 31.3 |
Bilirubin (mg/dL) | 0.8 ± 0.6 | 0.8 ± 0.3 | 0.8 ± 0.9 |
GGT (U/L) | 151.4 ± 122.6 | 143.6 ± 114.8 | 162.1 ± 113.2 |
Albumin (g/dL) | 4.0 ± 0.4 | 4.0 ± 0.3 | 4.0 ± 0.4 |
PT (s) | 13.5 ± 0.7 | 13.5 ± 0.7 | 13.5 ± 0.7 |
Hb (g/L) | 139.3 ± 27.3 | 138.8 ± 24.0 | 140.0 ± 31.6 |
WBC (G/L) | 10.0 ± 15.9 | 10.0 ± 16.2 | 10.0 ± 15.7 |
Platelet (G/L) | 230.5 ± 74.4 | 243.2 ± 77.9 | 213.0 ± 66.2 |
Region | Nucleotide | Amino Acid | Genotype B n= 62 | Genotype C n = 45 | p Value |
---|---|---|---|---|---|
PreS1 (2848–3204) | A2962G | N38E | 60 (96.8) | 0 | <0.001 * |
C2964A | N38E | 60 (96.8) | 0 | <0.001 * | |
C3026A | A60V | 61 (98.4) | 44 (97.8) | 0.818 * | |
S (155–835) | A162G | N3S | 1 (1.6) | 45 (100) | <0.001 * |
C531T | T126I | 0 | 25 (55.6) | <0.001 * | |
T766A | S204R | 11 (17.7) | 0 | 0.002 * | |
X (1374–1838) Enhancer II (1685–773) | G1721A | No change | 3 (4.8) | 39 (86.7) | <0.001 ** |
X (1374–1838) BCP (1751–1769) | A1762T | K130M | 32 (51.6) | 43 (95.6) | <0.001 * |
G1764A | V131I | 31 (50) | 43 (95.6) | <0.001 * | |
A1762T + G1764A | 31 (50) | 42 (93.3) | <0.001 * | ||
A1775G | No change | 1 (1.6) | 24 (53.3) | <0.001 * | |
Precore (1814–1900) | T1858C | No change | 1 (1.6) | 41 (91.1) | <0.001 * |
G1896A | W28Stop | 46 (74.2) | 2 (4.4) | 0.000 * | |
Polymerase (2307–1623) Putative Nar mutation | G287A | S53N | 47 (75.8) | 0 | <0.001 * |
A286G-G287A | S53D | 7 (11.3) | 0 | 0.021 * | |
G748A | V207M | 11 (17.7) | 0 | 0.002 * | |
T766A | S213T | 10 (16.1) | 0 | 0.005 * | |
T791A | F221Y | 59 (95.2) | 5 (11.1) | <0.001 * | |
A841C-T843C | N238H | 62 (100) | 0 | <0.001 * | |
A841C-A842C | N238T | 0 | 11 (24.4) | <0.001 * | |
A842C | |||||
A895G | S256G | 12 (19.4) | 0 | 0.001 * | |
Polymerase (2307–1623) Pretreatment mutation | T499C | Y124H | 61 (98.4) | 4 (8.9) | <0.001 * |
A799G | I224V | 61 (98.4) | 28 (62.2) | <0.001 * |
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Ho, P.T.; Balzanelli, M.G.; Distratis, P.; Lazzaro, R.; Tran, D.K.; Nguyen, K.C.D.; Bui, T.M.; Nguyen, T.T.; Pham, S.T.; Nguyen, H.S.D.; et al. Characteristics of Hepatitis B Virus Genotype and Sub-Genotype in Hepatocellular Cancer Patients in Vietnam. Diagnostics 2022, 12, 2393. https://doi.org/10.3390/diagnostics12102393
Ho PT, Balzanelli MG, Distratis P, Lazzaro R, Tran DK, Nguyen KCD, Bui TM, Nguyen TT, Pham ST, Nguyen HSD, et al. Characteristics of Hepatitis B Virus Genotype and Sub-Genotype in Hepatocellular Cancer Patients in Vietnam. Diagnostics. 2022; 12(10):2393. https://doi.org/10.3390/diagnostics12102393
Chicago/Turabian StyleHo, Phat Tan, Mario Giosuè Balzanelli, Pietro Distratis, Rita Lazzaro, Duy Khanh Tran, Kieu C. D. Nguyen, Tri Minh Bui, Thinh Tien Nguyen, Son Truong Pham, Huy Song Dinh Nguyen, and et al. 2022. "Characteristics of Hepatitis B Virus Genotype and Sub-Genotype in Hepatocellular Cancer Patients in Vietnam" Diagnostics 12, no. 10: 2393. https://doi.org/10.3390/diagnostics12102393
APA StyleHo, P. T., Balzanelli, M. G., Distratis, P., Lazzaro, R., Tran, D. K., Nguyen, K. C. D., Bui, T. M., Nguyen, T. T., Pham, S. T., Nguyen, H. S. D., Tran, V. T., Ho, T. T., Dipalma, G., Inchingolo, F., Quek, C., Pham, H. T., Isacco, C. G., Santacroce, L., & Pham, V. H. (2022). Characteristics of Hepatitis B Virus Genotype and Sub-Genotype in Hepatocellular Cancer Patients in Vietnam. Diagnostics, 12(10), 2393. https://doi.org/10.3390/diagnostics12102393