Foot-and-mouth disease virus (FMDV), like other RNA viruses, exhibits high mutation rates during replication that have been suggested to be of adaptive value. However, even though genetic variation in RNA viruses and, more specifically, FMDV has been extensively examined during virus replication in a wide variety of in vitro cell cultures, very little is known regarding the generation and effects of genetic variability of virus replication in the natural host under experimental conditions and no genetic data are available regarding the effects of serial passage in natural hosts. Here, we present the results of 20 serial contact transmissions of the highly pathogenic, pig-adapted O Taiwan 97 (O Tw97) isolate of FMDV in swine. We examined the virus genomic consensus sequences for a total of 37 full-length viral genomes recovered from 20 in vivo passages. The characteristics and distributions of changes in the sequences during the series of pig infections were analyzed in comparison to the O Tw97 genomes recovered from serially infected BHK-21 cell cultures. Unexpectedly, a significant reduction of virulence upon pig passages was observed, and finally, interruption of the viral transmission chain occurred after the14th pig passage (T14). Virus was, however, isolated from the tonsils and nasal swabs of the asymptomatic T15 pigs at 26 days postcontact, consistent with a natural establishment of the carrier state previously described only for ruminants. Surprisingly, the region encoding the capsid protein VP1 (1D) did not show amino acid changes during in vivo passages. These data demonstrate that contact transmission of FMDV O Tw97 in pigs mimics the fitness loss induced by the bottleneck effect, which was previously observed by others during plaque-to-plaque FMDV passage in vitro, suggesting that unknown mechanisms of virulence recovery might be necessary during the evolution and perpetuation of FMDV in nature.Foot-and-mouth disease (FMD) has a high economical impact, affecting domestic and wild cloven-hoofed animal species worldwide (reviewed in references 2, 3, 24, and 46). The etiological agent FMD virus (FMDV) of Picornaviridae occurs as seven distinct serotypes and multiple subtypes, reflecting significant genetic and antigenic heterogeneity. In the field, this heterogeneity is reflected by the lack of cross-protection even between intraserotype variants (2, 3, 46). VP1 (1D), the highly variable FMDV capsid protein with roles in virus entry, immunity, and serotype specificity, has been the subject of extensive comparative sequence analysis (reviewed in reference 22). These studies have shown cocirculation of FMDV genotypes in single outbreaks, with genotypes usually grouping into geographically and genetically distinct lineages (less than 15% nucleotide differences) known as topotypes (41). With the expansion of FMDV genomic databases, however, evidence is accumulating for the inadequacy of VP1 analysis alone for epidemiological studies and for the importance of recombination in FMDV evolution (4,20,23).The sel...