Splicing of these W repeat transcripts produces a short intron and a long intron (Fig. 1), both of which accumulate to high abundance in EBV-infected human B cells. Indeed, ebv-sisRNA-1 is the third most abundantly produced EBV RNA after EBER1 and EBER2, which are highly expressed in EBV-infected cells., The presence of these RNAs in a pathogenic form of latency suggests roles in EBV-associated cancers. The short W repeat intron, rather than being spliced and rapidly degraded, persists after splicing and is the third most abundant EBV-produced small ncRNA in latency III. Nucleotides 4 to 26 of ebv-sisRNA-1 form a short hairpin loop that presents a Uridine-rich sequence motif (a possible platform for protein interactions) into the loop. The remainder of the sequence is unlikely to form stable RNA structure. This unstructured stretch of sequence may be exposed to allow for interactions with nucleic acids or other proteins. The sisRNA sequence is ~100% conserved in EBV strains and homology extends to include other lymphocryptoviruses. The hairpin structure is also conserved and includes structure-preserving mutations in its stem. Ebv-sisRNA-2 is generated from the long W repeat intron. Evidence of stable and conserved RNA structure covers ~40% of this RNA and one region can fold into a remarkably long (586 nt) and thermodynamically stable hairpin loop (Fig. 2). In addition to EBV strains, where the hairpin is ~100% conserved in sequence, this structure is also found in other lymphocrypoviruses. Despite high divergence of sequence between these homologous RNAs, the long hairpin structure is well conserved. This suggests that this RNA plays an important functional role in ebv-sisRNA-2. The size of ebv-sisRNA-2 (2,791 nt) more closely resembles that the HHV Latency Associated Transcript) and may perhaps play a similar role in the maintenance of virus latency.