1. Magnius L, Mason WS, Taylor J, Kann M, Glebe D, Dény P, et al.
ICTV virus taxonomy profile: hepadnaviridae. J Gen Virol. 2020;
101:571–2.
2. Nassal M. HBV cccDNA: viral persistence reservoir and key
obstacle for a cure of chronic hepatitis B. Gut. 2015;64:1972–84.
3. Shi Y, Zheng M. Hepatitis B virus persistence and reactivation.
BMJ. 2020;370:m2200.
4. Seeger C, Mason WS. Molecular biology of hepatitis B virus
infection. Virology. 2015;479-480:672–86.
5. Sadiea RZ, Sultana S, Chaki BM, Islam T, Dash S, Akter S, et al.
Phytomedicines to target hepatitis B virus DNA replication: current
limitations and future approaches. Int J Mol Sci. 2022;23:1617.
6. Littlejohn M, Locarnini S, Yuen L. Origins and evolution of
hepatitis B virus and hepatitis D virus. Cold Spring Harb Perspect
Med. 2016;6:a021360.
7. Gilbert C, Feschotte C. Genomic fossils calibrate the long-term
evolution of hepadnaviruses. PLoS Biol. 2010;8:e1000495.
8. Osiowy C, Giles E, Tanaka Y, Mizokami M, Minuk GY. Molecular
evolution of hepatitis B virus over 25 years. J Virol. 2006;80:
10307–4.
9. Suh A, Brosius J, Schmitz J, Kriegs JO. The genome of a
Mesozoic paleovirus reveals the evolution of hepatitis B viruses.
Nat Commun. 2013;4:1791.
10. Suzuki T, Masui N, Kajino K, Saito I, Miyamura T. Detection and
mapping of spliced RNA from a human hepatoma cell line
transfected with the hepatitis B virus genome. Proc Natl Acad Sci
USA. 1989;86:8422–6.
11. Terré S, Petit M-A, Bréchot C. Defective hepatitis B virus
particles are generated by packaging and reverse transcription of
spliced viral RNAs in vivo. J Virol. 1991;65:5539–43.
12. Günther S, Sommer G, Iwanska A, Will H. Heterogeneity and
common features of defective hepatitis B virus genomes derived
from spliced pregenomic RNA. Virology. 1997;238:363–71.
HEPATOLOGY COMMUNICATIONS
13. Sommer G, van Bömmel F, Will H. Genotype-specific synthesis
and secretion of spliced hepatitis B virus genomes in hepatoma
cells. Virology. 2000;271:371–81.
14. Kremsdorf D, Lekbaby B, Bablon P, Sotty J, Augustin J,
Schnuriger A, et al. Alternative splicing of viral transcripts: the
dark side of HBV. Gut. 2021;70:2373–82.
15. Suzuki Y, Maekawa S, Komatsu N, Sato M, Tatsumi A, Miura M,
et al. HBV preS deletion mapping using deep sequencing
demonstrates a unique association with viral markers. PLOS
ONE. 2019;14:e0212559.
16. Betz-Stablein BD, Töpfer A, Littlejohn M, Yuen L, Colledge D,
Sozzi V, et al. Single-molecule sequencing reveals complex
genome variation of hepatitis B virus during 15 years of chronic
infection following liver transplantation. J Virol. 2016;90:
7171–83.
17. Yamashita T, Takeda H, Takai A, Arasawa S, Nakamura F,
Mashimo Y, et al. Single-molecular real-time deep sequencing
reveals the dynamics of multi-drug resistant haplotypes and
structural variations in the hepatitis c virus genome. Sci Rep.
2020;10:2651.
18. Takeda H, Ueda Y, Inuzuka T, Yamashita Y, Osaki Y, Nasu A,
et al. Evolution of multi-drug resistant HCV clones from preexisting resistant-associated variants during direct-acting antiviral therapy determined by third-generation sequencing. Sci
Rep. 2017;7:45605.
19. Lee GH, Wasser S, Lim SG. Hepatitis B pregenomic RNA
splicing—the products, the regulatory mechanisms and its
biological significance. Virus Res. 2008;136:1–7.
20. Abraham TM, Lewellyn EB, Haines KM, Loeb DD. Characterization of the contribution of spliced RNAs of hepatitis B virus to
DNA synthesis in transfected cultures of Huh7 and HepG2 cells.
Virology. 2008;379:30–7.
21. Huang C-C, Kuo T-M, Yeh C-T, Hu C-p, Chen Y-L, Tsai Y-L,
et al. One single nucleotide difference alters the differential
expression of spliced RNAs between HBV genotypes A and D.
Virus Res. 2013;174:18–26.
22. Chen J, Wu M, Wang F, Zhang W, Wang W, Zhang X, et al.
Hepatitis B virus spliced variants are associated with an impaired
response to interferon therapy. Sci Rep. 2015;5:16459.
23. Lam AM, Ren S, Espiritu C, Kelly M, Lau V, Zheng L, et al.
Hepatitis B virus capsid assembly modulators, but not nucleoside
analogs, inhibit the production of extracellular pregenomic RNA
and spliced RNA variants. Antimicrob Agents Chemother. 2017;
61:e00680–00617.
24. Lim CS, Sozzi V, Luciani F, Littlejohn M, Revill PA, Brown CM.
Quantitative analysis of the splice variants expressed by the
major hepatitis B virus genotypes. Microb Genom. 2021;7:
mgen000492.
25. Luk KC, Gersch J, Harris BJ, Holzmayer V, Mbanya D, Sauleda
S, et al. More DNA and RNA of HBV SP1 splice variants are
detected in genotypes B and C at low viral replication. Sci Rep.
2021;11:23838.
26. Kandpal M, Samal J, Biswas B, Negi A, Mishra VC, Tyagi N,
et al. Enhanced hepatitis B virus (HBV) pre-genomic RNA levels
and higher transcription efficiency of defective HBV genomes.
J Gen Virol. 2015;96:3109–17.
27. Nishijima N, Marusawa H, Ueda Y, Takahashi K, Nasu A, Osaki
Y, et al. Dynamics of hepatitis B virus quasispecies in
association with nucleos(t)ide analogue treatment determined
by ultra-deep sequencing. PLoS ONE. 2012;7:e35052.
28. Hayer J, Rodriguez C, Germanidis G, Deléage G, Zoulim F,
Pawlotsky J-M, et al. Ultradeep pyrosequencing and molecular
modeling identify key structural features of hepatitis B virus
RNase H, a putative target for antiviral intervention. J Virol. 2014;
88:574–82.
29. Lowe CF, Merrick L, Harrigan PR, Mazzulli T, Sherlock CH,
Ritchie G. Implementation of next-generation sequencing for
SMRT SEQUENCING FOR HBV QUASISPECIES
30.
31.
32.
33.
34.
35.
36.
37.
38.
39.
hepatitis B Virus resistance testing and genotyping in a clinical
microbiology laboratory. J Clin Microbiol. 2016;54:127–33.
Gencay M, Vermeulen M, Neofytos D, Westergaard G, Pabinger
S, Kriegner A, et al. Substantial variation in the hepatitis B
surface antigen (HBsAg) in hepatitis B virus (HBV)-positive
patients from South Africa: Reliable detection of HBV by the
Elecsys HBsAg II assay. J Clin Virol. 2018;101:38–43.
Chevaliez S, Rodriguez C, Poiteau L, Soulier A, Donati F, DartyMercier M, et al. Primary resistance of hepatitis B virus to
nucleoside and nucleotide analogues. J Viral Hepat. 2019;26:
278–86.
Hayashi S, Murakami S, Omagari K, Matsui T, Iio E, Isogawa M,
et al. Characterization of novel entecavir resistance mutations.
J Hepatol. 2015;63:546–3.
Han Y, Zhang Y, Mei Y, Wang Y, Liu T, Guan Y, et al. Analysis of
hepatitis B virus genotyping and drug resistance gene mutations
based on massively parallel sequencing. J Virol Methods. 2013;
193:341–7.
Rajoriya N, Combet C, Zoulim F, Janssen HLA. How viral genetic
variants and genotypes influence disease and treatment outcome of chronic hepatitis B. Time for an individualised
approach? J Hepatol. 2017;67:1281–97.
Bruni R, Villano U, Taffon S, Equestre M, Madonna E, Chionne
P, et al. Retrospective analysis of acute HBV infections occurred
in 1978–79 and 1994– 95 in North-East Italy: increasing
prevalence of BCP/pre-core mutants in sub-genotype D3. BMC
Infect Dis. 2020;20:78.
Wu I-C, Liu W-C, Chang T-T. Applications of next-generation
sequencing analysis for the detection of hepatocellular carcinoma-associated hepatitis B virus mutations. J Biomed Sci.
2018;25:51.
Teng C-F, Huang H-Y, Li T-C, Shyu W-C, Wu H-C, Lin C-Y, et al.
A next-generation sequencingbased platform for quantitative
detection of hepatitis B virus pre-S mutants in plasma of
hepatocellular carcinoma patients. Sci Rep. 2018;8:14816.
Anastasiou OE, Widera M, Verheyen J, Korth J, Gerken G,
Helfritz FA, et al. Clinical course and core variability in HBV
infected patients without detectable anti-HBc antibodies. J Clin
Virol. 2017;93:46–52.
Anastasiou OE, Widera M, Westhaus S, Timmer L, Korth J,
Gerken G, et al. Clinical outcome and viral genome variability of
hepatitis b virus–induced acute liver failure. Hepatology. 2019;
69:993–1003.
15
40. Cheng J-H, Liu W-C, Chang T-T, Hsieh S-Y, Tseng VS.
Detecting exact breakpoints of deletions with diversity in hepatitis
B viral genomic DNA from next-generation sequencing data.
Methods. 2017;129:24–32.
41. Jia J, Liang X, Chen S, Wang H, Li H, Fang M, et al. Nextgeneration sequencing revealed divergence in deletions of the
preS region in the HBV genome between different HBV-related
liver diseases. J Gen Virol. 2017;98:2748–58.
42. Liu W-C, Wu I-C, Lee Y-C, Lin C-P, Cheng J-H, Lin Y-J, et al.
Hepatocellular carcinoma-associated single-nucleotide variants and
deletions identified by the use of genome-wide high-throughput
analysis of hepatitis B virus. J Pathol. 2017;243:176–92.
43. Sauvage V, Boizeau L, Candotti D, Vandenbogaert M, ServantDelmas A, Caro Vr, et al. Early MinION™nanopore singlemolecule sequencing technology enables the characterization of
hepatitis B virus genetic complexity in clinical samples. PLOS
ONE. 2018;13:e0194366.
44. Yang Z-T, Huang S-Y, Chen L, Liu F, Cai X-H, Guo Y-F, et al.
Characterization of full-length genomes of hepatitis B virus
quasispecies in sera of patients at different phases of infection.
J Clin Microbiol. 2015;53:2201–14.
45. Gao S, Duan Z-P, Coffin CS. Clinical relevance of hepatitis B
virus variants. World J Hepatol. 2015;7:1086–96.
46. Xue Y, Wang MJ, Huang SY, Yang ZT, Yu DM, Han Y, et al.
Characteristics of CpG Islands and their quasispecies of fulllength hepatitis B virus genomes from patients at different
phases of infection. SpringerPlus. 2016;5:1630.
47. Yamani LN, Yano Y, Utsumi T, Juniastuti, Wandono H, Widjanarko
D, et al. Ultradeep sequencing for detection of quasispecies
variants in the major hydrophilic region of hepatitis B virus in
Indonesian patients. J Clin Microbiol. 2015;53:3165–75.
How to cite this article: Arasawa S, Takeda H,
Takai A, Iguchi E, Eso Y, Shimizu T, et al.
Evolutional transition of HBV genome during the
persistent infection determined by single-molecule real-time sequencing. Hepatol Commun.
2023;7:e0047. https://doi.org/10.1097/HC9.000
0000000000047
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