Recent studies revealed that posttranslational modifications (e.g., phosphorylation and methylation) of the small hepatitis delta antigen (SHDAg) are required for hepatitis delta virus (HDV) replication from antigenomic to genomic RNA. The phosphorylation of SHDAg at serine 177 (Ser 177 ) is involved in this step, and this residue is crucial for interaction with RNA polymerase II (RNAP II), the enzyme assumed to be responsible for antigenomic RNA replication. This study demonstrated that SHDAg dephosphorylated at Ser 177 interacted preferentially with hypophosphorylated RNAP II (RNAP IIA), which generally binds at the transcription initiation sites. In contrast, the Ser 177 -phosphorylated counterpart (pSer 177 -SHDAg) exhibited preferential binding to hyperphosphorylated RNAP II (RNAP IIO). In addition, RNAP IIO associated with pSer 177 -SHDAg was hyperphosphorylated at both the Ser 2 and Ser 5 residues of its carboxyl-terminal domain (CTD), which is a hallmark of the transcription elongation isoform. Moreover, the RNAP II CTD kinase inhibitor 5,6-dichloro-1--D-ribofuranosyl-benzimidazole (DRB) not only blocked the interaction between pSer 177 -SHDAg and RNAP IIO but also inhibited HDV antigenomic replication. Our results suggest that the phosphorylation of SHDAg at Ser 177 shifted its affinity toward the RNA RNAP IIO isoform and thus is a switch for HDV antigenomic RNA replication from the initiation to the elongation stage.The hepatitis delta virus (HDV) is a negative-stranded RNA virus with a 1.7-kb circular, single-stranded RNA genome. The single-stranded RNA genome is folded into an unbranched rod-like structure because of a high degree of intramolecular self-complementarity (10,32,44,63). HDV is a defective virus (58) that requires surface antigen (HBsAg) of helper hepatitis B virus (HBV) for virion assembly and infectivity (3,58,60). In addition to the HDV RNA genome and the HBV envelope, the HDV particle also contains hepatitis delta antigen (HDAg), which is the sole known protein encoded by the open reading frame of the HDV RNA (26, 48). There are two forms of HDAg, the small HDAg of 195 amino acids (SHDAg; 24 kDa) and the large HDAg of 214 amino acids (LHDAg; 27 kDa) (64). The amino acid sequences of these two forms of HDAg are identical, with the exception that LHDAg is 19 amino acids longer than SHDAg at its C terminus, which results from an RNA-editing event during viral replication (40). Although these two isoforms of HDAg share similar amino acid sequences, they play different functions in the life cycle of HDV. SHDAg is an essential activator of HDV RNA replication (9, 33), while LHDAg promotes virion assembly (6).The replication of HDV RNA is independent from its helper HBV (33) and does not involve any DNA intermediates (10). It occurs in the nucleus, probably via a double-rolling-circle mechanism (42, 62). As neither HDV nor mammalian cells encode an RNA-dependent RNA polymerase (RdRp), the replication of HDV RNA may rely on a redirection of a host DNA-dependent RNA polymerase to become the ...