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

Abstract

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 (KCB) in order to distinguish it from other subtype B clusters. Genetic distance analysis suggested that the KCB cluster was more homogeneous and clearly distinctive from the non-Korean clade subtype B (NKCB). Comparison of consensus amino acid sequences from KCB and NKCB revealed that characteristic KCB signature amino acid patterns composed of 11 amino acid residues, whose frequencies in the KCB were significantly higher than in the NKCB. The KCB signature amino acid residues were critical in identifying KCB from NKCB, since substitution of the NKCB sequences with KCB signature amino acids relocated them to the Koran clade, and vice versa.

Timing and evolution of the most recent common ancestor of the Korean clade HIV subtype B based on Nef and Vif sequences

“…Even with the same data set, different analytical methods estimated different dates (Lukashov and Goudsmit, 2002). Using two genes (nef and vif) and two methods (BA and ML) for each gene, we were able to obtain very similar results, may be due to high similarity of the KCB sequences compared to other subtype B sequences (Park et al, 2006(Park et al, , 2008. The Korean clade diversified 8 to 17 years after the emergence of the subtype B.…”

“…The presence of the Korean clade has been supported by further studies based on molecular phylogenetic analyses of pol (Sung et al, 2001), nef (Kang et al, 1998;Lee et al, 2003), env (Kim et al, 1999a(Kim et al, , 1999b, and vif (Park et al, 2006) genes. The Korean clade, a subcluster of HIV-1 subtype B, accounted for more than 60% of all HIV isolated from Koreans and exhibited unique nucleotide and amino acid sequences that distinguished the Korean clade from others (Park et al, 2006(Park et al, , 2008 HIV-1 is classified into three major groups, M, N, and O, and group M is further divided into several subtypes whose regional distribution is well known. Using the most recent common ancestor (MRCA) sequences inferred from known sampling date and assuming a constant rate of evolution, it was suggested that M group was first established around 1931 (Korber et al, 2000).…”

“…All available nucleotide sequences of nef (n=422) and vif (n=233) genes of HIV-1 isolated from Korean patients were retrieved from NCBI GenBank database as described before (Park et al, 2006(Park et al, , 2008. Relevant foreign sequences with more than 90% homology with Korean isolates were obtained from NCBI GenBank database by BLAST search and reference sequences were obtained from Los Alamos HIV Database (http://hiv-web.lanl.gov).…”

“…And once separated, the Korean clade appeared to have undergone different evolutionary pathway from the other subtype B and the hallmark of the evolutionary pathway seems to be the KCB-specific signature amino acid pattern (Park et al, 2006(Park et al, , 2008. HIV-1 nef gene encodes a transactivating factor that may reduce or increase viral replication depending on cell type (Welker et al, 1996;Levy, 1998).…”

“…CTL escape mutations could be positively selected within an individual host, and would be characteristic for specific HLA class I alleles across an HLA-diverse host population (Moore et al, 2002). Previously we analyzed substitution events in the KCB and some of the nonsynonymous substitutions were identified to constitute signature amino acid residues whose frequencies were significantly higher among KCB (Park et al, 2006(Park et al, , 2007(Park et al, , 2008. Some of the signature amino acids of the KCB nef could be located to HLA-restricted CTL epitope motifs where the amino acids are enriched in the presence of a specific HLA allele thus presumably represent escape variants (Brumme et al, 2007).…”