cis-acting RNA elements required for replication of bovine viral diarrhea virus–hepatitis C virus 5′ nontranslated region chimeras

Abstract

Pestiviruses, such as bovine viral diarrhea virus (BVDV), share many similarities with hepatitis C virus (HCV) yet are more amenable to virologic and genetic analysis. For both BVDV and HCV, translation is initiated via an internal ribosome entry site (IRES). Besides IRES function, the viral 5′ nontranslated regions (NTRs) may also contain cis-acting RNA elements important for viral replication. A series of chimeric RNAs were used to examine the function of the BVDV 5′ NTR. Our results show that: (1) the HCV and the encephalomyocarditis virus (EMCV) IRES element can functionally replace that of BVDV; (2) two 5′ terminal hairpins in BVDV genomic RNA are important for efficient replication; (3) replacement of the entire BVDV 5′ NTR with those of HCV or EMCV leads to severely impaired replication; (4) such replacement chimeras are unstable and efficiently replicating pseudorevertants arise; (5) pseudorevertant mutations involve deletion of 5′ sequences and/or acquisition of novel 5′ sequences such that the 5′ terminal 3–4 bases of BVDV genome RNA are restored. Besides providing new insight into functional elements in the BVDV 5′ NTR, these chimeras may prove useful as pestivirus vaccines and for screening and evaluation of anti-HCV IRES antivirals.