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Abstract
There have been attempts to use consensus sequences or ancestor sequences for development vaccines against viruses with high diversity and variation. In this study, we generated and compared consensus sequences and ancestor sequences of nef and vif genes of HIV-1 isolated from Koreans. Phylogenetic analyses revealed that majorities of the Korean isolates were clustered to form the Korean clade within subtype B (KcB) where foreign isolates were not included. Consensus sequences inferred from the KcB as well as from all Korean isolates were almost identical but significantly different from subtype B consensus sequence or HIV-1 consensus sequence. The genetic distances from one of the Korean isolates to the other Korean isolates were much longer than to the consensus or ancestor sequences deduced from Korean isolates but similar to those of subtype B or HIV-1. Moreover, the genetic distances from the Korean isolates to the consensus sequences were shorter than to the ancestor sequences both in nef and vif genes. Thus, the consensus sequences may be useful in developing Korean-specific HIV-1 vaccine.
References
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Figure 1.
Composition of the Korean clade (KcB), non-Korean clade (NKcB) within subtype B and other subtypes of the HIV-1 isolated from Koreans. Amino acid sequences of nef and vif genes of HIV-1 isolated from Koreans were obtained from NCBI GenBank database. The sequences were multiple-aligned using ClustalX and subjected to phylogenetic analyses using Phylip package. KcB is, by definition, a subcluster of subtype B where foreign or references sequences are excluded. (A) nef gene, (B) vif gene.
Figure 2.
Consensus and ancestor sequences of nef. Aligned nef amino acid sequences belonged to specific cluster were used to generated consensus or ancestor sequences. For comparison, references consensus or ancestor sequences including subtype B and HIV-1 were obtained from HIV-1 Database.
Figure 3.
Location of the consensus or ancestor sequences in the phylogenetic tree. Phylogenetic tree was constructed from HIV-1 nef (A) or vif (B) amino acid sequences together with the inferred consensus or ancestor sequences.
Table 1.
Genetic distances from consensus, ancestor or individual sequences to the sequences of the Korean isolates: HIV-1 nef gene
Table 2.
Genetic distances from consensus, ancestor or individual sequences to the sequences of the Korean isolates: HIV-1 vif gene
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