Murine coronaviruses undergo RNA recombination at a very high frequency. We have obtained a series of recombinant viruses using neutralizing monoclonal antibodies in conjunction with temperature-sensitive markers. All of the recombinants obtained have a crossover within gene C, which encodes the peplomer protein of the virus. The genetic structure of these recombinants suggests that the antigenic regions recognized by these neutralizing monoclonal antibodies are localized on the carboxyl-terminal one-third of the peplomer protein. Since the two monoclonal antibodies used are also associated with the critical determinants of virus neuropathogenicity, we conclude that both the neutralizing antibody binding sites and determinants of pathogenicity are localized at the carboxyl-terminal one-third of the peplomer. The variation of crossover sites in different recombinant viruses also allowed precise mapping of additional antigenic sites. RNA recombination thus presents a powerful genetic tool, and the carboxylterminal localization of the biological functions of peplomers suggests a distinct conformation of these viral membrane proteins.Mouse hepatitis virus (MHV), a coronavirus, is an enveloped virus containing two envelope glycoproteins, El and E2, and a nucleocapsid protein, N (1). The N protein has a molecular weight of 60,000 and is closely associated with viral RNA. The El glycoprotein has a molecular weight of -25,000 and probably serves as a matrix protein. The E2 glycoprotein, a 180-kDa heterodimer, forms the projecting spikes or peplomers on the surface of the virus particle and is involved in the attachment of virus to target cells, in the induction of cell-to-cell fusion, and in the elicitation of neutralizing antibodies (1-3). Competitive binding studies have identified at least six major antigenic sites on the E2, three of which are involved in virus neutralization (refs. 4 MHV contains a single piece of single-stranded RNA genome of positive polarity (9). The RNA contains at least seven genes, termed genes A through G in the 5'-3' order, based on the finding that, in infected cells, six subgenomic and one genomic mRNAs are expressed (10). These mRNAs have a 3'-coterminal, nested-set structure, i.e., the sequence of each mRNA is contained entirely within the next larger mRNA (10). Only the 5'-specific portions, which do not overlap with the next smaller mRNAs, are translated. Furthermore, each mRNA contains a leader sequence of '70 nucleotides, which is derived from the 5' end of the genome and joined to the mRNAs by a mechanism of "leader-primed transcription" (11,12). Despite the fact that MHV genome is a single, nonsegmented RNA, our laboratory has demonstrated that MHV can undergo RNA-RNA recombination at an extremely high frequency (13), reminiscent of the genetic reassortment of viruses with segmented RNA genomes. This observation suggests that fragmented RNA intermediates might be generated during replication of MHV RNA, probably by a mechanism of discontinuous and nonprocessive RNA synth...