There are at least thirteen subtypes of the meningococcal virus, but only five of them cause the vast majority of serious disease. Both vaccines protect against the same four of the five subtypes. Fortunately, the four subtypes account for the majority of disease in adults and adolescents, while the fifth subtype, serogroup B, accounts for half of the infections in infants.
Thus, the effectiveness of the vaccine depends on which serogroup the patient is exposed to. If the serogroup is in one of the vaccines, then the vaccines will be tremendously helpful, protecting 90 percent of recipients. If it is a different serogroup, the vaccine will not help at all.
The protection from the older Menomune vaccine wanes more quickly than other similar vaccines, often fading after three to five years. The hope is that the newer vaccine, Menactra, will provide more long lasting protection. However, as it only was approved in 2005, the long-term protection is still unknown.