Hepatitis B virus preS2Δ38–55 variants: A newly identified risk factor for hepatocellular carcinoma

Schweitzer, 2015, Estimations of worldwide prevalence of chronic hepatitis B virus infection: a systematic review of data published between 1965 and 2013, Lancet, 386, 1546, 10.1016/S0140-6736(15)61412-X Maucort-Boulch, 2018, Fraction and incidence of liver cancer attributable to hepatitis B and C viruses worldwide: liver cancer attributable to hepatitis viruses worldwide, Int J Cancer, 142, 2471, 10.1002/ijc.31280 Norder, 2004, Genetic diversity of hepatitis B virus strains derived worldwide: genotypes, subgenotypes, and HBsAg subtypes, Intervirology, 47, 289, 10.1159/000080872 Hussain, 2003, Rapid and sensitive assays for determination of hepatitis B virus (HBV) genotypes and detection of HBV precore and core promoter variants, J Clin Microbiol, 41, 3699, 10.1128/JCM.41.8.3699-3705.2003 Rajoriya, 2017, How viral genetic variants and genotypes influence disease and treatment outcome of chronic hepatitis B. Time for an individualised approach?, J Hepatol, 67, 1281, 10.1016/j.jhep.2017.07.011 Hayer, 2013, HBVdb: a knowledge database for hepatitis B virus, Nucleic Acids Res, 41, D566, 10.1093/nar/gks1022 Malve, 2017, Impact of deletions and mutations in hepatitis B virus envelope proteins on serological profile and clinical evolution, Virus Res, 238, 141, 10.1016/j.virusres.2017.06.028 Pollicino, 2014, Hepatitis B virus PreS/S gene variants: pathobiology and clinical implications, J Hepatol, 61, 408, 10.1016/j.jhep.2014.04.041 Wild, 2009, A model of interaction: aflatoxins and hepatitis viruses in liver cancer aetiology and prevention, Cancer Lett, 286, 22, 10.1016/j.canlet.2009.02.053 Gouas, 2009, The aflatoxin-induced TP53 mutation at codon 249 (R249S): biomarker of exposure, early detection and target for therapy, Cancer Lett, 286, 29, 10.1016/j.canlet.2009.02.057 Mendy, 2010, Hepatitis B viral load and risk for liver cirrhosis and hepatocellular carcinoma in the Gambia, West Africa, J Viral Hepat, 17, 115, 10.1111/j.1365-2893.2009.01168.x Kirk, 2004, The Gambia liver cancer study: infection with hepatitis B and C and the risk of hepatocellular carcinoma in West Africa, Hepatology, 39, 211, 10.1002/hep.20027 Mahale, 2019, Hepatitis D virus infection, cirrhosis and hepatocellular carcinoma in the Gambia, J Viral Hepat, 26, 738, 10.1111/jvh.13065 Kirk, 2005, 249(ser) TP53 mutation in plasma DNA, hepatitis B viral infection, and risk of hepatocellular carcinoma, Oncogene, 24, 5858, 10.1038/sj.onc.1208732 Lemoine, 2016, Acceptability and feasibility of a screen-and-treat programme for hepatitis B virus infection in the Gambia: the Prevention of Liver Fibrosis and Cancer in Africa (PROLIFICA) study, Lancet Glob Health, 4, e559, 10.1016/S2214-109X(16)30130-9 Shimakawa, 2015, Birth order and risk of hepatocellular carcinoma in chronic carriers of hepatitis B virus: a case-control study in the Gambia, Liver Int, 35, 2318, 10.1111/liv.12814 Lemoine, 2016, The gamma-glutamyl transpeptidase to platelet ratio (GPR) predicts significant liver fibrosis and cirrhosis in patients with chronic HBV infection in West Africa, Gut, 65, 1369, 10.1136/gutjnl-2015-309260 Ghosh, 2010, Unique hepatitis B virus subgenotype in a primitive tribal community in eastern India, J Clin Microbiol, 48, 4063, 10.1128/JCM.01174-10 Ghosh, 2013, New HBV subgenotype D9, a novel D/C recombinant, identified in patients with chronic HBeAg-negative infection in eastern India, J Viral Hepat, 20, 209, 10.1111/j.1365-2893.2012.01655.x Madeira, 2019, The EMBL-EBI search and sequence analysis tools APIs in 2019, Nucleic Acids Res, 47, W636, 10.1093/nar/gkz268 Crooks, 2004, WebLogo: a sequence logo generator, Genome Res, 14, 1188, 10.1101/gr.849004 Schultz, 2012, jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus, Nucleic Acids Res, 40, W193, 10.1093/nar/gks414 Ranwez, 2011, MACSE: multiple Alignment of Coding SEquences accounting for frameshifts and stop codons, PLoS One, 6, e22594, 10.1371/journal.pone.0022594 Criscuolo, 2010, BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evol Biol, 10, 210, 10.1186/1471-2148-10-210 Guindon, 2010, New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst Biol, 59, 307, 10.1093/sysbio/syq010 Kalyaanamoorthy, 2017, ModelFinder: fast model selection for accurate phylogenetic estimates, Nat Methods, 14, 587, 10.1038/nmeth.4285 Letunic, 2016, Interactive Tree of Life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Res, 44, W242, 10.1093/nar/gkw290 Shimakawa, 2016, Natural history of chronic HBV infection in West Africa: a longitudinal population-based study from the Gambia, Gut, 65, 2007, 10.1136/gutjnl-2015-309892 Kew, 2005, Increased hepatocarcinogenic potential of hepatitis B virus genotype A in Bantu-speaking sub-Saharan Africans, J Med Virol, 75, 513, 10.1002/jmv.20311 Chen, 2006, High prevalence and mapping of pre-S deletion in hepatitis B virus carriers with progressive liver diseases, Gastroenterology, 130, 1153, 10.1053/j.gastro.2006.01.011 Yeung, 2011, Association of hepatitis B virus pre-S deletions with the development of hepatocellular carcinoma in chronic hepatitis B, J Infect Dis, 203, 646, 10.1093/infdis/jiq096 Chen, 2018, Hepatitis B virus pre-S/S variants in liver diseases, World J Gastroenterol, 24, 1507, 10.3748/wjg.v24.i14.1507 Liu, 2017, Hepatocellular carcinoma-associated single-nucleotide variants and deletions identified by the use of genome-wide high-throughput analysis of hepatitis B virus, J Pathol, 243, 176, 10.1002/path.4938 Lereau, 2012, Interactions between hepatitis B virus and aflatoxin B1: effects on p53 induction in HepaRG cells, J Gen Virol, 93, 640, 10.1099/vir.0.032482-0 Marchio, 2018, Droplet digital PCR detects high rate of TP53 R249S mutants in cell-free DNA of middle African patients with hepatocellular carcinoma, Clin Exp Med, 18, 421, 10.1007/s10238-018-0502-9 Su, 2018, Liquid biopsies for hepatocellular carcinoma, Transl Res, 201, 84, 10.1016/j.trsl.2018.07.001 Gerken, 1991, Hepatitis B defective virus with rearrangements in the PreS gene during chronic HBV infection, Virology, 183, 555, 10.1016/0042-6822(91)90984-J Hsieh, 2004, Pre-S mutant surface antigens in chronic hepatitis B virus infection induce oxidative stress and DNA damage, Carcinogenesis, 25, 2023, 10.1093/carcin/bgh207 Hsieh, 2015, Hepatitis B virus pre-S2 mutant large surface protein inhibits DNA double-strand break repair and leads to genome instability in hepatocarcinogenesis, J Pathol, 236, 337, 10.1002/path.4531 Su, 2008, Ground glass hepatocytes contain pre-S mutants and represent preneoplastic lesions in chronic hepatitis B virus infection, J Gastroenterol Hepatol, 23, 1169, 10.1111/j.1440-1746.2008.05348.x Su, 2014, The emerging role of hepatitis B virus pre-S2 deletion mutant proteins in HBV tumorigenesis, J Biomed Sci, 21, 98, 10.1186/s12929-014-0098-7 Jia, 2018, Characterization of small genomic regions of the hepatitis B virus should be performed with more caution, Virol J, 15, 188, 10.1186/s12985-018-1100-x Pourkarim, 2010, Are hepatitis B virus “subgenotypes” defined accurately?, J Clin Virol, 47, 356, 10.1016/j.jcv.2010.01.015 McNaughton, 2020, Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences, J Gen Virol, 101, 271, 10.1099/jgv.0.001387