Characterization and signature pattern analysis of Korean clade HIV-1 using nef gene sequences.

Phylogenetic studies of the HIV-1 gene sequences isolated from Korean patients have suggested that most of Korean isolates belong to the subtype B strain. This study aims to characterize the Korean clade by molecular phylogenetic analysis using all of the Korean nef gene sequences registered in the NCBI GenBank (N=422), in addition to 41 reference strains and 94 foreign isolates. Through phylogenetic analyses, we verified that most of the Korean isolates belonged to the subtype B, where 78.8 % are clustered exclusively of foreign isolates. This cluster has been named the Korean clade subtype B (K_cB) in order to distinguish it from other subtype B clusters. Genetic distance analysis suggested that the K_cB cluster was more homogeneous and clearly distinctive from the non-Korean clade subtype B (NK_cB). Comparison of consensus amino acid sequences from K_cB and NK_cB revealed that characteristic K_cB signature amino acid patterns composed of 11 amino acid residues, whose frequencies in the K_cB were significantly higher than in the NK_cB. The K_cB signature amino acid residues were critical in identifying K_cB from NK_cB, since substitution of the NK_cB sequences with K_cB signature amino acids relocated them to the Koran clade, and vice versa. [ABSTRACT FROM AUTHOR]