{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T18:46:57Z","timestamp":1776451617167,"version":"3.51.2"},"reference-count":47,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2023,2,6]],"date-time":"2023-02-06T00:00:00Z","timestamp":1675641600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The study aimed to characterize the genotype and subgenotypes of HBV circulating in Saudi Arabia, the presence of clinically relevant mutations possibly associated with resistance to antivirals or immune escape phenomena, and the possible impact of mutations in the structural characteristics of HBV polymerase. Plasma samples from 12 Saudi Arabian HBV-infected patients were analyzed using an in-house PCR method and direct sequencing. Saudi patients were infected with mainly subgenotype D1. A number of mutations in the RT gene (correlated to antiviral resistance) and within and outside the major hydrophilic region of the S gene (claimed to influence immunogenicity and be related to immune escape) were observed in almost all patients. Furthermore, the presence of mutations in the S region caused a change in the tertiary structure of the protein compared with the consensus region. Clinical manifestations of HBV infection may change dramatically as a result of viral and host factors: the study of mutations and protein-associated cofactors might define possible aspects relevant for the natural and therapeutic history of HBV infection.<\/jats:p>","DOI":"10.3390\/v15020458","type":"journal-article","created":{"date-parts":[[2023,2,7]],"date-time":"2023-02-07T02:28:17Z","timestamp":1675736897000},"page":"458","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Molecular and Genetic Characterization of Hepatitis B Virus (HBV) among Saudi Chronically HBV-Infected Individuals"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8814-0953","authenticated-orcid":false,"given":"Mariantonietta","family":"Di Stefano","sequence":"first","affiliation":[{"name":"Department of Clinical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, 71122 Foggia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5969-3890","authenticated-orcid":false,"given":"Giuseppina","family":"Faleo","sequence":"additional","affiliation":[{"name":"Department of Clinical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, 71122 Foggia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8160-2588","authenticated-orcid":false,"given":"Thomas","family":"Leitner","sequence":"additional","affiliation":[{"name":"Theoretical Biology & Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2984-9003","authenticated-orcid":false,"given":"Wei","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"},{"name":"Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA"},{"name":"Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amna","family":"Hassan","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, King Fahd Hospital of the University, Al-Khobar 31952, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4646-6717","authenticated-orcid":false,"given":"Marwan J.","family":"Alwazzeh","sequence":"additional","affiliation":[{"name":"College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34221, Saudi Arabia"},{"name":"Infectious Disease Division, King Fahd Hospital of the University, Al-Khobar 34217, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jos\u00e8 R.","family":"Fiore","sequence":"additional","affiliation":[{"name":"Department of Clinical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, 71122 Foggia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6371-3997","authenticated-orcid":false,"given":"Mona","family":"Ismail","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, King Fahd Hospital of the University, Al-Khobar 31952, Saudi Arabia"},{"name":"College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34221, Saudi Arabia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4342-6904","authenticated-orcid":false,"given":"Teresa A.","family":"Santantonio","sequence":"additional","affiliation":[{"name":"Department of Clinical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, 71122 Foggia, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,2,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1016\/j.jhep.2017.07.011","article-title":"How viral genetic variants and genotypes influence disease and treatment outcome of chronic hepatitis B. Time for an individualised approach?","volume":"67","author":"Rajoriya","year":"2017","journal-title":"J. Hepatol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1016\/S0140-6736(09)60207-5","article-title":"Hepatitis B virus infection","volume":"373","author":"Liaw","year":"2009","journal-title":"Lancet"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"11630","DOI":"10.3748\/wjg.v20.i33.11630","article-title":"Molecular mechanism of hepatitis B virus-induced hepatocarcinogenesis","volume":"20","author":"Tarocchi","year":"2014","journal-title":"World J. Gastroenterol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"435","DOI":"10.2147\/JHC.S307962","article-title":"The Mechanisms of HBV-Induced Hepatocellular Carcinoma","volume":"ume 8","author":"Jiang","year":"2021","journal-title":"J. Hepatocell. Carcinoma"},{"key":"ref_5","unstructured":"World Health Organization (2022, September 02). Global Progress Report on HIV, Viral Hepatitis, and Sexually Transmitted Infections. Available online: https:\/\/www.who.int\/publications\/i\/item\/9789240027077."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/j.cld.2016.06.006","article-title":"Epidemiology of Hepatitis B Virus Infection and Impact of Vaccination on Disease","volume":"20","author":"Nelson","year":"2016","journal-title":"Clin. Liver Dis."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"73","DOI":"10.4103\/sjg.SJG_421_18","article-title":"Hepatitis B care pathway in Saudi Arabia: Current situation, gaps and actions","volume":"25","author":"Aljumah","year":"2019","journal-title":"Saudi J. Gastroenterol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"277","DOI":"10.15537\/smj.2019.3.23585","article-title":"Temporal trends in the incidence and demographics of cancers, communicable diseases, and non-communicable diseases in Saudi Arabia over the last decade","volume":"40","author":"Herzallah","year":"2019","journal-title":"Saudi Med. J."},{"key":"ref_9","first-page":"104051","article-title":"Molecular epidemiology, phylogenetic analysis and genotype distribution of hepatitis B virus in Saudi Arabia: Predominance of genotype D1","volume":"77","author":"Pourkarim","year":"2019","journal-title":"Infect. Genet. Evol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"194","DOI":"10.4103\/sjg.SJG_447_18","article-title":"Greater prevalence of comorbidities with increasing age: Cross-sectional analysis of chronic hepatitis B patients in Saudi Arabia","volume":"25","author":"Sanai","year":"2019","journal-title":"Saudi J. Gastroenterol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/S1386-6532(02)00049-5","article-title":"The virological and clinical significance of mutations in the overlapping envelope and polymerase genes of hepatitis B virus","volume":"25","author":"Torresi","year":"2002","journal-title":"J. Clin. Virol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1111\/j.1440-1746.2010.06541.x","article-title":"The clinical implications of hepatitis B virus genotype: Recent advances","volume":"26","author":"Lin","year":"2011","journal-title":"J. Gastroenterol. Hepatol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"145","DOI":"10.3748\/wjg.v22.i1.145","article-title":"Overview of hepatitis B virus mutations and their implications in the management of infection","volume":"22","author":"Caligiuri","year":"2016","journal-title":"World J. Gastroenterol."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Lazarevic, I., Banko, A., Miljanovic, D., and Cupic, M. (2019). Immune-Escape Hepatitis B Virus Mutations Associated with Viral Reactivation upon Immunosuppression. Viruses, 11.","DOI":"10.3390\/v11090778"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Inoue, J., Nakamura, T., and Masamune, A. (2019). Roles of Hepatitis B Virus Mutations in the Viral Reactivation after Immunosuppression Therapies. Viruses, 11.","DOI":"10.3390\/v11050457"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"71","DOI":"10.12998\/wjcc.v4.i3.71","article-title":"Hepatitis B surface antigen escape mutations: Indications for initiation of antiviral therapy revisited","volume":"4","author":"Leong","year":"2016","journal-title":"World J. Clin. Cases"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.1053\/j.gastro.2009.08.063","article-title":"Hepatitis B Virus Resistance to Nucleos(t)ide Analogues","volume":"137","author":"Zoulim","year":"2009","journal-title":"Gastroenterology"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1016\/j.jhep.2008.07.038","article-title":"The profile of mutational clusters associated with lamivudine resistance can be constrained by HBV genotypes","volume":"50","author":"Svicher","year":"2009","journal-title":"J. Hepatol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1016\/j.antiviral.2011.08.013","article-title":"Characterization of drug-resistance mutations in HBV D-genotype chronically infected patients, na\u00efve to antiviral drugs","volume":"92","author":"Salpini","year":"2011","journal-title":"Antivir. Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"14","DOI":"10.3748\/wjg.v13.i1.14","article-title":"Hepatitis B virus taxonomy and hepatitis B virus genotypes","volume":"13","author":"Schaefer","year":"2007","journal-title":"World J. Gastroenterol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"W557","DOI":"10.1093\/nar\/gki352","article-title":"PHYML Online\u2014A web server for fast maximum likelihood-based phylogenetic inference","volume":"33","author":"Guindon","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"315","DOI":"10.6026\/97320630006315","article-title":"Structure prediction and functional characterization of secondary metabolite proteins of Ocimum","volume":"6","author":"Roy","year":"2011","journal-title":"Bioinformation"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"100014","DOI":"10.1016\/j.crmeth.2021.100014","article-title":"Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations","volume":"1","author":"Zheng","year":"2021","journal-title":"Cell Rep. Methods"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"W291","DOI":"10.1093\/nar\/gkx366","article-title":"COFACTOR: Improved protein function prediction by combining structure, sequence and protein\u2013protein interaction information","volume":"45","author":"Zhang","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"W174","DOI":"10.1093\/nar\/gkv342","article-title":"I-TASSER server: New development for protein structure and function predictions","volume":"43","author":"Yang","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1177\/135965350901400416","article-title":"Adefovir dipivoxil resistance patterns in patients with lamivudine-resistant chronic hepatitis B","volume":"14","author":"Santantonio","year":"2009","journal-title":"Antivir. Ther."},{"key":"ref_28","first-page":"202","article-title":"The Molecular and Structural Basis of HBV-resistance to Nucleos(t)ide Analogs","volume":"2","author":"Gupta","year":"2014","journal-title":"J. Clin. Transl. Hepatol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Tuteja, A., Siddiqui, A.B., Madan, K., Goyal, R., Sreenivas, V., Kaur, N., Panda, S.K., Narayanasamy, K., and Subodh, S. (2014). Mutation Profiling of the Hepatitis B Virus Strains Circulating in North Indian Population. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0091150"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1128\/JCM.01073-09","article-title":"Selection and Counterselection of the rtI233V Adefovir Resistance Mutation during Antiviral Therapy","volume":"48","author":"Schildgen","year":"2010","journal-title":"J. Clin. Microbiol."},{"key":"ref_31","first-page":"81","article-title":"Prevalence of hepatitis B virus genotype in Saudi Arabia: A preliminary report","volume":"27","author":"Imambaccus","year":"2008","journal-title":"Indian J. Gastroenterol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"176","DOI":"10.4103\/sjg.SJG_515_16","article-title":"Prevalence and molecular characterization of hepatitis D virus in Saudi Arabia: A single-center study","volume":"23","author":"Jamjoom","year":"2017","journal-title":"Saudi J. Gastroenterol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2864","DOI":"10.1002\/ijc.28307","article-title":"Novel point mutations and mutational complexes in the enhancer II, core promoter and precore regions of hepatitis B virus genotype D1 associated with hepatocellular carcinoma in Saudi Arabia","volume":"133","author":"Khan","year":"2013","journal-title":"Int. J. Cancer"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1016\/j.sjbs.2016.03.003","article-title":"Sequence analysis of sub-genotype D hepatitis B surface antigens isolated from Jeddah, Saudi Arabia","volume":"25","author":"Alakilli","year":"2018","journal-title":"Saudi J. Biol. Sci."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1186\/1743-422X-7-160","article-title":"Hepatitis B virus genotypes and precore and core mutants in UAE patients","volume":"7","author":"Alfaresi","year":"2010","journal-title":"Virol. J."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.ajg.2013.04.002","article-title":"Hepatitis B virus in the Arab world: Where do we stand?","volume":"14","author":"Gasim","year":"2013","journal-title":"Arab. J. Gastroenterol."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Zehender, G., Ebranati, E., Gabanelli, E., Shkjezi, R., Lai, A., Sorrentino, C., Presti, A.L., Basho, M., Bruno, R., and Tanzi, E. (2012). Spatial and Temporal Dynamics of Hepatitis B Virus D Genotype in Europe and the Mediterranean Basin. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0037198"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1111\/j.1365-2893.2005.00584.x","article-title":"Hepatitis B virus: Significance of genotypes","volume":"12","author":"Schaefer","year":"2005","journal-title":"J. Viral Hepat."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1002\/jmv.20677","article-title":"Phylogenetic relatedness and genetic diversity of hepatitis B virus isolates in Eastern India","volume":"78","author":"Banerjee","year":"2006","journal-title":"J. Med. Virol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1829","DOI":"10.1099\/vir.0.83660-0","article-title":"D2: Major subgenotype of hepatitis B virus in Russia and the Baltic region","volume":"89","author":"Tallo","year":"2008","journal-title":"J. Gen. Virol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"762","DOI":"10.4314\/ahs.v17i3.19","article-title":"Hepatitis B virus DNA polymerase gene polymorphism based prediction of genotypes in chronic HBV patients from Western India","volume":"17","author":"Chavan","year":"2017","journal-title":"Afr. Health Sci."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"583","DOI":"10.4254\/wjh.v7.i3.583","article-title":"Variations and mutations in the hepatitis B virus genome and their associations with clinical characteristics","volume":"7","author":"Yano","year":"2015","journal-title":"World J. Hepatol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"8078","DOI":"10.1038\/s41598-019-44604-6","article-title":"Potential resistant mutations within HBV reverse transcriptase sequences in nucleos(t)ide analogues-experienced patients with hepatitis B virus infection","volume":"9","author":"Zhang","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1016\/j.jhep.2007.06.011","article-title":"Pooled analysis of amino acid changes in the HBV polymerase in patients from four major adefovir dipivoxil clinical trials","volume":"47","author":"Miller","year":"2007","journal-title":"J. Hepatol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1007\/s12041-007-0027-6","article-title":"Mutations in the S gene region of hepatitis B virus genotype D in Turkish patients","volume":"86","author":"Barsgan","year":"2007","journal-title":"J. Genet."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Hossain, M.G., and Ueda, K. (2017). Investigation of a Novel Hepatitis B Virus Surface Antigen (HBsAg) Escape Mutant Affecting Immunogenicity. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0167871"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e04332","DOI":"10.1016\/j.heliyon.2020.e04332","article-title":"In silico functional and structural characterization of hepatitis B virus PreS\/S-gene in Iranian patients infected with chronic hepatitis B virus genotype D","volume":"6","author":"Khodadad","year":"2020","journal-title":"Heliyon"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/2\/458\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T18:25:48Z","timestamp":1760120748000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/2\/458"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,6]]},"references-count":47,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2023,2]]}},"alternative-id":["v15020458"],"URL":"https:\/\/doi.org\/10.3390\/v15020458","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,2,6]]}}}