VP1 is the most suitable region for use in the identification of enterovirus. Although VP1 sequencing methods may vary, it is necessary to agree on a common strategy of sequence analysis. Identification of a strain type may be achieved by three different approaches: pairwise sequence alignment, multiple-sequence alignment, and phylogenetic inference. Other methods are also available, but they are not simple enough to be performed at a virology laboratory. best performances when used with the correct criteria. Other commercial and expensive programs did not achieve the same performances, making them less suitable for molecular typing of enteroviruses. Finally, although phylogenetic inference is the most demanding method in terms of knowledge of the user, it remained the best option analyzed.Enteroviruses (EVs) are a large genus belonging to the Picornaviridae family, and 64 immunologically distinct serotypes are known to cause infections in humans. They are the etiological agents responsible for several diseases (poliomyelitis, acute myocarditis, and aseptic meningitis) and play an important role in common chronic diseases, including dilated cardiomyopathy and insulin-dependent diabetes mellitus. Identification of EVs is essential for epidemiological surveillance, identification of polioviruses, the study of correlations between EV subtypes and diseases, identification of new EV types, and adequate treatment of EV infections in neonates and immunodeficient patients (for a complete review, see reference 15). Although the serotype identity can be determined by neutralization of infectivity with serotype-specific antisera, individual typing of all 64 serotypes by neutralization is clearly impractical. To overcome this problem, intersecting pools of individual antisera which allow the identification of a serotype were developed. Despite that, the method is still time-consuming, labor-intensive, and costly; and the supply of antisera is limited. Moreover, there are frequent problems related to untypeable EVs that have been associated with mixtures of EVs, the existence of certain EV serotypes that cannot be identified with intersecting pools, the formation of aggregates (9), and the existence of antigenic variants of recognized EVs (13). Finally, some unrecognized serotypes are also untypeable by this standard method.Because of these problems, several methods were developed for the molecular characterization of the genus (1,(5)(6)(7)17). The coupling of reverse transcription and amplification of the enteroviral RNA by PCR, followed by direct sequencing of the amplified products, is the general approach. Some of these methods analyzed the 5Ј noncoding, the VP2, or the 3D region of the EVs genome; but the sequence did not always correlate with the corresponding serotype (1, 10, 18). The VP1 region was the most suitable target due to the high correlation between serotypes and sequences and the availability of a large database of EVs sequences (17). Two methods were developed for the typing of EV strains by partial sequen...