Biological and clinical significance of hepatitis B virus RNA splicing: an update

Hepatitis B virus (HBV) persistent infection remains a major public health issue. Long-lasting persistence/occult carriage is associated with a strong inhibition of HBV replication and viral protein synthesis involving the complex interplay of viral and/or cellular control mechanisms. The characterization of viral RNA metabolism of pregenomic and subgenomic HBV RNAs should provide insights into some of these molecular mechanisms. Singly and multiply spliced HBV transcripts from pgRNA and preS2/S mRNA have been identified. Constitutive and cryptic splicing signals vary in number and location according to genotypes and individual strain sequences. Sixteen and four splice variants of the pgRNA and the preS2/S mRNA have been characterized so far, respectively. It is critical that the majority of viral RNAs escapes the cellular splicing machinery and is exported by a splicing-independent mechanism. This suggests that HBV splicing is not a constitutive process but it is precisely regulated by cis-acting genetic elements and cellular and/or viral trans-acting factors controlling both activation of cryptic splicing sites and silencing of constitutive splicing sites. Modulation of alternate splicing events seems to be involved in the severity and progression of liver disease in HBV chronic carriers. Spliced pgRNA variants generate viral defective particles and encode for additional HBV proteins whose still unclear functions were associated with viral replication control and innate and/or adaptive immunity escape. Additional studies are required to characterize host factors, additional cis-acting elements, RNA-RNA, RNA-protein and protein-protein interactions involved in the complex regulatory mechanisms underlying HBV RNA splicing. Understanding the regulation of HBV splicing might provide valuable indications on its potential implication in the long-term persistence of HBV in occult carriers. Nevertheless, the conservation of splicing sites, the complex modulation of splicing during infection, and unique proteins encoded by spliced viral RNAs strongly suggest a functional role of splicing in the HBV life cycle. The present review aims to supplement HBV RNA splicing knowledge previously published (Allain JP, Fu Y, Li C, Raimondo G. editors, Occult hepatitis B infection, 1st ed. Science Press, Beijing, China) with the recent data from the literature.