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The mechanisms involved in the clinical progression of HDV are not fully elucidated. Few studies relate mutations to clinical implications, which makes this variable extremely relevant for research into HDV-3, a genotype associated with worse clinical progression. The aim of this study was to analyze mutations in complete genome sequences of HDV-3 isolated in the Brazilian Western Amazon. During 2010 to 2023, 35 hepatitis Delta patients with mild or advanced fibrosis gave serum samples that were submitted to conventional PCR and sequencing. Synonymous and non-synonymous mutations were analyzed along the delta antigen sequence based on the reference strain NC_076103.1. N-terminal and C-terminal regions of Large HDAg, molecular modeling and docking analyses were performed. 114 non-synonymous substitutions were identified in 76 positions along the HDAg-L. To synonymous mutations, 46 substitutions were found in 44 nucleotide sites. S\/L8P\/Q\/M was the most frequent mutation among the advanced fibrosis group. The D46E and A70T mutation was more observed among patients with increased AST. These associations showed statistically significant p-values. Mutations in the N-terminal region of Large HDAg led to minor conformational changes. The C-terminal region indicates moderate structural differences caused by the mutations. The binding conformation of Large HDAg with Mutant2C exhibiting the most stable interaction, as suggested by its docking score. This study shows some evidence of the influence of HDAg mutations in relation to clinical significance, providing insights for further, longitudinal research.<\/jats:p>","DOI":"10.1007\/s00705-026-06697-z","type":"journal-article","created":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T17:29:46Z","timestamp":1785432586000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comprehensive Analysis of Mutations in the Hepatitis Delta Virus Genome Based on Full-Length Sequencing in Individuals Infected with Genotype 3 in Brazil"],"prefix":"10.1007","volume":"171","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0203-0409","authenticated-orcid":false,"given":"T\u00e1rcio Peixoto","family":"Roca","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jackson Alves","family":"da Silva Queiroz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Maisa","family":"Passos-Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mayara Torquato Lima","family":"da Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eug\u00eania","family":"de Castro-Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lourdes Maria Pinheiro","family":"Borzacov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan Miguel","family":"Villalobos-Salcedo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deusilene","family":"Vieira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7644-8969","authenticated-orcid":false,"given":"Livia Melo","family":"Villar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,30]]},"reference":[{"key":"6697_CR1","doi-asserted-by":"publisher","first-page":"313","DOI":"10.5501\/wjv.v4.i4.313","volume":"4","author":"C Cunha","year":"2015","unstructured":"Cunha C, Tavanez JP, Gudima S (2015) Hepatitis delta virus: A fascinating and neglected pathogen. 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