Antibodies to the class 2/3 OMPs (PorB) are bactericidal and antigenic diversity between these proteins forms the basis of the current serotyping classification. The variable regions of the porB gene from the 13 serotype strains expressing class 3 OMP have been examined and a panel of oligonucleotide probes for identification and classification of strains using genetic techniques developed. We have developed a PCR system to examine the molecular epidemiology of meningococcal meningitis in Brazil by amplifying porB directly from cerebrospinal fluid with subsequent oligonucleotide probe hybridization to genotype the porB variable regions. We are applying this system to CSF samples from 100 patients with meningitis from Brazil. Using both probe hybridization and direct sequencing, we have identified regions of the porB gene from an unusual Chilean strain (501) which are similar to each of the two prototype type 4 and type 15 strains. Rabbit immunization studies using this strain show immunodominance of individual epitopes corresponding to particular variable regions in individual animals. Bactericidal assays coincide with the data from Western blots. Bactericidal activity has been shown against a strain which does not express class 1 OMP (PorA), and a strain which does not express the class 1 or the class 5 OMPs, suggesting that the variable region specific anti-VR1 PorB antibodies may be functional. These studies will help in our understanding of how host immune pressure causes selective changes in meningococcal surface proteins, and will help in out understanding of the nature of non-capsular protective immunity to meningococcal disease. These studies have resulted in development of a genotyping system that may be used to evaluate cases of meningococcal disease in vaccine trials, including culture negative suspected cases.