{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T17:42:27Z","timestamp":1790790147096,"version":"4.1.0"},"reference-count":26,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2022,6,5]],"date-time":"2022-06-05T00:00:00Z","timestamp":1654387200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Dutch Research Council Open Technology Program grant","award":["15783"],"award-info":[{"award-number":["15783"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Hepatitis B Virus (HBV) encoded miRNAs were previously described and suggested to play a role in HBV replication and pathogenesis. In this study we aim to identify novel HBV encoded miRNAs in plasma and liver tissue samples from chronic hepatitis B (CHB) patients and determine their role in CHB pathogenesis and HBV replication. RNA next generation sequencing was performed on plasma and liver tissue samples from ten CHB patients and uninfected controls. The interaction of the potential miRNA-like structures with the RNA-induced silencing complex (RISC) was determined using RNA immunoprecipitation. Expression levels of the HBV encoded miRNAs were measured in liver tissue samples derived from a conformation cohort. The effect of HBV encoded miRNAs overexpression on HBV replication, expression of predicted target genes, and induction of interferon stimulated genes in cell lines were assessed. Three potential miRNA-like structures transcribed by HBV were identified in liver tissue, of which one miRNA, HBV-miR-6, was recognized using RISC. HBV-miR-6 expression was demonstrated in liver tissue samples from 52 of the 87 CHB patients. HBV-miR-6 levels correlated with hepatic HBV-DNA and plasma HBsAg levels. Overexpression of HBV-miR-6 in vitro did not affect HBV replication, and predicted both target genes expression and interferon stimulated genes expression after stimulation. A potential novel HBV encoded miRNA was identified and validated in liver tissue from CHB patients. It is suggested that HBV-miR-6 may play a role in the process of viral excretion or particle formation in vivo.<\/jats:p>","DOI":"10.3390\/v14061223","type":"journal-article","created":{"date-parts":[[2022,6,5]],"date-time":"2022-06-05T10:47:11Z","timestamp":1654426031000},"page":"1223","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Identification of a Novel HBV Encoded miRNA Using Next Generation Sequencing"],"prefix":"10.3390","volume":"14","author":[{"given":"Vladimir","family":"Loukachov","sequence":"first","affiliation":[{"name":"Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands"},{"name":"Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karel A.","family":"van Dort","sequence":"additional","affiliation":[{"name":"Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands"},{"name":"Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Louis","family":"Jansen","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Amsterdam UMC Location University of Amsterdam, 1105 AZ Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henk W.","family":"Reesink","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Hepatology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9429-7754","authenticated-orcid":false,"given":"Neeltje A.","family":"Kootstra","sequence":"additional","affiliation":[{"name":"Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands"},{"name":"Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105 AZ Amsterdam, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,6,5]]},"reference":[{"key":"ref_1","unstructured":"World Health Organization (2021, December 20). Hepatitis B Key Facts. Available online: https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/hepatitis-b."},{"key":"ref_2","unstructured":"GBD 2017 Causes of Death Collaborators (2018). Global, regional, and national age-sex-specific mortality for 282 causes of death in 195 countries and territories, 1980\u20132017: A systematic analysis for the Global Burden of Disease Study 2017. Lancet, 392, 1736\u20131788."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1016\/S0140-6736(70)90926-8","article-title":"Virus-like particles in serum of patients with Australia-antigen-associated hepatitis","volume":"1","author":"Dane","year":"1970","journal-title":"Lancet"},{"key":"ref_4","unstructured":"Thomas, H.C., Lok, A.S.F., Locarnini, S.A., and Zuckerman, A.J. (2014). Other hepadnaviridae [Avihepadnaviridae (DHBV) and Orthohepadnaviridae (WHV)]. Viral Hepatitis, Wiley-Blackwell. [4th ed.]."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"672","DOI":"10.1016\/j.virol.2015.02.031","article-title":"Molecular biology of hepatitis B virus infection","volume":"479\u2013480","author":"Seeger","year":"2015","journal-title":"Virology"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/j.virusres.2007.12.024","article-title":"Hepatitis B viruses: Reverse transcription a different way","volume":"134","author":"Nassal","year":"2008","journal-title":"Virus Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1016\/j.jhep.2016.01.027","article-title":"Overview of hepatitis B viral replication and genetic variability","volume":"64","author":"Tong","year":"2016","journal-title":"J. Hepatol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.antiviral.2015.06.020","article-title":"Core protein: A pleiotropic keystone in the HBV lifecycle","volume":"121","author":"Zlotnick","year":"2015","journal-title":"Antivir. Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"691766","DOI":"10.3389\/fimmu.2021.691766","article-title":"The Functions of Hepatitis B Virus Encoding Proteins: Viral Persistence and Liver Pathogenesis","volume":"12","author":"Zhao","year":"2021","journal-title":"Front. Immunol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1053\/jhep.2003.50453","article-title":"Exploring the biological basis of hepatitis B e antigen in hepatitis B virus infection","volume":"38","author":"Milich","year":"2003","journal-title":"Hepatology"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1101\/gr.082701.108","article-title":"Most mammalian mRNAs are conserved targets of microRNAs","volume":"19","author":"Friedman","year":"2009","journal-title":"Genome Res."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Gallo, A., Miceli, V., Bulati, M., Iannolo, G., Contino, F., and Conaldi, P.G. (2020). Viral miRNAs as Active Players and Participants in Tumorigenesis. Cancers, 12.","DOI":"10.3390\/cancers12020358"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Kincaid, R., and Sullivan, C.S. (2012). Virus-encoded microRNAs: An overview and a look to the future. PLoS Pathog., 8.","DOI":"10.1371\/journal.ppat.1003018"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Yang, X., Li, H., Sun, H., Fan, H., Hu, Y., Liu, M., Li, X., and Tang, H. (2017). Hepatitis B Virus-Encoded MicroRNA Controls Viral Replication. J. Virol., 91.","DOI":"10.1128\/JVI.01919-16"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1093\/jmcb\/mjz104","article-title":"An HBV-encoded miRNA activates innate immunity to restrict HBV replication","volume":"12","author":"Zhao","year":"2020","journal-title":"J. Mol. Cell Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"232","DOI":"10.2174\/2211536608666191104105334","article-title":"Hepatitis B Virus-Encoded MicroRNA (HBV-miR-3) Regulates Host Gene PPM1A Related to Hepatocellular Carcinoma","volume":"9","author":"Chavalit","year":"2020","journal-title":"Microrna"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/S2468-1253(17)30221-2","article-title":"Peg-interferon plus nucleotide analogue treatment versus no treatment in patients with chronic hepatitis B with a low viral load: A randomised controlled, open-label trial","volume":"2","author":"Jansen","year":"2017","journal-title":"Lancet Gastroenterol. Hepatol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"6172","DOI":"10.1038\/s41598-017-06352-3","article-title":"Human intrahepatic CD69 + CD8+ T cells have a tissue resident memory T cell phenotype with reduced cytolytic capacity","volume":"7","author":"Stelma","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"D127","DOI":"10.1093\/nar\/gkz757","article-title":"miRDB: An online database for prediction of functional microRNA targets","volume":"48","author":"Chen","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/s13059-019-1629-z","article-title":"Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data","volume":"20","author":"Liu","year":"2019","journal-title":"Genome Biol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"8463","DOI":"10.1128\/JVI.72.11.8463-8471.1998","article-title":"A third-generation lentivirus vector with a conditional packaging system","volume":"72","author":"Dull","year":"1998","journal-title":"J. Virol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Mitra, B., Wang, J., Kim, E.S., Mao, R., Dong, M., Liu, Y., Zhang, J., and Guo, H. (2019). Hepatitis B Virus Precore Protein p22 Inhibits Alpha Interferon Signaling by Blocking STAT Nuclear Translocation. J. Virol., 93.","DOI":"10.1128\/JVI.00196-19"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1016\/S0168-8278(00)80308-6","article-title":"Interferon-induced gene expression and signaling in human hepatoma cell lines","volume":"33","author":"Keskinen","year":"2000","journal-title":"J. Hepatol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"960","DOI":"10.1016\/j.jhep.2019.12.019","article-title":"A dual role for hepatocyte-intrinsic canonical NF-kappaB signaling in virus control","volume":"72","author":"Namineni","year":"2020","journal-title":"J. Hepatol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1779","DOI":"10.1002\/hep.29348","article-title":"Hepatitis B virus evades innate immunity of hepatocytes but activates cytokine production by macrophages","volume":"66","author":"Cheng","year":"2017","journal-title":"Hepatology"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"S71","DOI":"10.1016\/j.jhep.2016.01.026","article-title":"Adaptive immunity in HBV infection","volume":"64","author":"Bertoletti","year":"2016","journal-title":"J. Hepatol."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/14\/6\/1223\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:24:39Z","timestamp":1760138679000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/14\/6\/1223"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,5]]},"references-count":26,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2022,6]]}},"alternative-id":["v14061223"],"URL":"https:\/\/doi.org\/10.3390\/v14061223","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,5]]}}}