## 3 Control of HDV RNA Editing
### Restriction of Editing to the amber/W Site  
Given the important role of dsRNA secondary structure in editing by ADAR1 and the high degree of base pairing in the HDV RNA unbranched rod structure, it is clear that potential exists for editing of sites other than the amber/W site. However, such non-specific editing could be harmful to the virus. Because HDAg functions as a multimer [37], deleterious mutations of the protein have the potential to act as dominant negative inhibitors of replication. In fact, we have shown such inhibition by mutant forms of HDAg that arose as a result of spurious editing when ADAR1 or ADAR2 were overexpressed [11]. Thus, it is not surprising that promiscuous editing does not occur during typical HDV replication [11,38]; indeed, in one study we determined that, on average, the amber/W site is edited 600-fold more efficiently than the other 337 adenosines in the RNA [38].  
There are three likely explanations for how HDV prevents editing from occurring at non-amber/W sites: (1) as indicated by the analysis of the type 1 amber/W site, although about 70% of bases are paired in the unbranched rod structure, this pairing is frequently disrupted by internal bulges and loops that limit ADAR binding; (2) the predicted secondary structure of type 1 RNA contains just 2 A-C mismatch pairs, which have been shown to be edited with the highest efficiency; (3) the frequency of GA dinucleotides, which are strongly disfavored for editing, is 60% higher than predicted based on a random distribution. Indeed, G is the 5' neighbor of 48% of adenosines and both of the adenosines present as A-C mismatch pairs have G as the 5' neighbor. In addition to the above effects that restrict the amount of editing at non-amber/W sites, HDV appears to be able to limit propagation of genomes that have been edited at these sites. We observed that editing of non-amber/W adenosines was strongly correlated with editing at the amber/W site on the same RNA [38]. Because edited RNAs encode HDAg-L, which cannot support HDV replication, such genomes are dead-end products of the virus replication cycle and virus particles containing them will not be infectious.  
It is important to note that, although the amount of editing that occurs at non-amber/W sites is very low relative to the amber/W site and does not likely contribute either positively or negatively to the replication cycle, such editing does occur at low levels during replication [39] and may contribute to the evolution of genetic changes in the virus that can affect the outcome of infection [40]. [PERSON] _et al._ were able to observe the susceptibility of additional sites to editing by using a vivid-like model in which replication of an HDAg-defective HDV genome was supported for one year by HDAg provided in _trans_[41]. Because sequence changes in this model system had no effect on HDAg and could accumulate over the course of the year, very high levels of editing were observed for a number of positions in the genome and antigenome. Thus, while in a typical analysis of editing following initiation of replication by transfecting cultured Huh7 cells, amber/W site editing reaches a maximum level of 25%-30% about 14 days posttransfection and editing at other sites is less than1% [38], in the Chang study the amber/W site was 100% edited and nine other sites were edited more than 50% [41]. It remains to be seen whether any of the additional editing sites identified in this study are preferential sites for editing during the course of HDV infection.