Virogenomics: a novel approach to antiviral drug discovery.

Target discovery in virology has been limited to the few open-reading frames encoded by viral genomes. However, several recent examples show that inhibiting host-cell proteins can prevent viral infection. The human genome sequence should, therefore, contain many more genes that are essential for viral propagation than viral genomes. A systematic approach to find these potential cellular antiviral targets is global host gene expression analysis using DNA microarrays. Several recent studies reveal both unique and common strategies by which viruses change the gene expression profile of the host cell. Moreover, work in progress shows that some of the host pathways discovered by expression profiling are important for viral replication. Thus, human genomics tools have the potential to deliver novel antiviral drugs.

Requirements for RNA replication of a poliovirus replicon by coxsackievirus B3 RNA polymerase.

A chimeric poliovirus type 1 (PV1) genome was constructed in which the 3D RNA polymerase (3D(pol)) coding sequences were replaced with those from coxsackievirus B3 (CVB3). No infectious virus was produced from HeLa cells transfected with the chimeric RNA. Processing of the PV1 capsid protein precursor was incomplete, presumably due to inefficient recognition of the P1 protein substrate by the chimeric 3CD proteinase containing CVB3 3D sequences. The ability of the chimeric RNA to replicate in the absence of capsid formation was measured after replacement of the P1 region with a luciferase reporter gene. No RNA synthesis was detected, despite efficient production of enzymatically active 3D(pol) from the 3D portion of the chimeric 3CD. The chimeric 3CD protein was unable to efficiently bind to the cloverleaf-like structure (CL) at the 5' end of PV1 RNA, which has been demonstrated previously to be required for viral RNA synthesis. The CVB3 3CD protein bound the PV1 CL as well as PV1 3CD. An additional chimeric PV1 RNA that contained CVB3 3CD sequences also failed to produce virus after transfection. Since processing of PV1 capsid protein precursors by the CVB3 3CD was again incomplete, a luciferase-containing replicon was also analyzed for RNA replication. The 3CD chimera replicated at 33 degrees C, but not at 37 degrees C. Replacement of the PV1 5'-terminal CL with that of CVB3 did not rescue the temperature-sensitive phenotype. Thus, there is an essential interaction(s) between 3CD and other viral P2 or P3 protein products required for efficient RNA replication which is not fully achieved between proteins from the two different members of the same virus genus.