Eleven clones of dengue virus 2 Mexican strain were selected by the size of their lytic plaques. Nucleotide sequences of the clones producing large plaques (D2ML2, D2ML3 and D2ML4) revealed 11 mutations, 10 of which were silent. The substitution at nucleotide 1168 (G-->C) generates one amino acid difference at residue 390 (Asp-->His) of the envelope protein (E). These clones showed high virulence in suckling mice when inoculated intracerebrally (> or = 70% mortality). However, the clones which showed small lytic plaques (D2MS1, D2MS2 and D2MS4) displayed a substitution from Asp-->Asn at the same position and had attenuated virulence. Based on these data, we suggest that substitution of Asp-->His at residue 390 perhaps affects a functionally important structural element that could be a determinant of dengue neurovirulence. This substitution falls in domain III of the E protein, which plays an important role in viral binding; therefore, we propose that the substitution affects virulence and cellular tropism.