genomic approaches as large-scale screening tools to identify genes that play important roles in the pathophysiology of pneumovirus infection. These elegant and simple tools will provide us with the means for thorough and systematic exploration of gene expression, both in the estab- Cytokine macroarray probed with radiolabelled cDNA generated from total RNA extracted from epithelial cells 48 h after RSV infection (upper panel) or 48 h after exposure to conditioned medium (lower panel). Signal intensity of each gene under each condition is compared. The arrow highlights the signal for human MIP-1α present at 12-fold higher concentration in infected epithelial cells compared with the uninfected controls. Sequence requirements for RNA strand transfer during nidovirus discontinuous subgenomic RNA synthesis Nidovirus subgenomic mRNAs contain a leader sequence derived from the 5′ end of the genome fused to different sequences (‘bodies’) derived from the 3′ end. Their generation involves a unique mechanism of discontinuous subgenomic RNA synthesis that resembles copy-choice RNA recombination. During this process, the nascent RNA strand is transferred from one site in the template to another, during either plus or minus strand synthesis, to yield subgenomic RNA molecules. Central to this process are transcription-regulating sequences (TRSs), which are present at both template sites and ensure the fidelity of strand transfer. Here we present results of a comprehensive co-variation mutagenesis study of equine arteritis virus TRSs, demonstrating that discontinuous RNA synthesis depends not only on base pairing between sense leader TRS and antisense body TRS, but also on the primary sequence of the body TRS. While the leader TRS merely plays a targeting role for strand transfer, the body TRS fulfils multiple functions. The sequences of mRNA leader–body junctions of TRS mutants strongly suggested that the discontinuous step occurs during minus strand synthesis. The genetic information of RNA viruses is organized very ef®ciently. Practically every nucleotide of their genome is utilized, either as protein-coding sequence or as cis-acting signals for translation, RNA synthesis or RNA encapsidation. As part of their genome expression strategy, several groups of positive-strand RNA (+RNA) viruses produce subgenomic (sg) mRNAs (reviewed by Miller and Koev, 2000) . The replication of their genomic RNA, which is also the mRNA for the viral replicase, is supplemented with the generation of sg transcripts to express structural and auxiliary proteins, which are encoded downstream of the replicase gene in the genome. Sg mRNAs of +RNA viruses are always 3¢-co-terminal with the genomic RNA, but different mechanisms are used for their synthesis.