Detection and characterization of subgenomic RNAs in hepatitis A virus particles

Defective viral particles containing deleted genomes were detected in harvests of cell cultures infected with various HAV isolates. The most prominent deletions were identified within the region of the genome coding for structural proteins. In this location three different deletions spanning nts 930–4380 (A), 1140–3820 (B), and 1370–3240 (C) were characterized. In addition to these internal deletions, various truncated RNAs were detected lacking either partially or completely the 3′ terminal region which is supposed to code for viral replicase. RNA molecules with internal deletions as well as those with 3′ terminal truncations could also be extracted directly from infected cells. During multiple consecutive passages of a given HAV strain, deletions A, B, and C accumulated and a quantitative increase of deleted RNAs occurred. Type and predominance of deletions varied with virus strains (CLF, GBM, MBB11/5, HM175, CR326, H141) and with the type of cells used for propagation (MRC-5, BGM, HELF, PLC/PRF/5). However, within the limits of the reliability of S1 analysis the endpoints of deletions A, B, and C were conserved. The mechanisms leading to formation of deletions remain unclear. Yet, some sequences flanking internal deletions showed homology with common splice signals and 3′ terminal truncations proved to be confined to a distinct region within the genome.