Abstract
We determined the earliest full-length HIV-1 gag gene sequences in 110 patients with HIV-1, including 20 hemophiliacs (HPs) and 90 local controls (LCs). The gag gene from stored sera was amplified using RT-PCR, and was subjected to direct sequencing. Phylogenetic analysis indicated that 94 and 16 sequences belonged to the Korean subclade of HIV-1 subtype B (KSB) and subtype B, respectively. A total of 12 signature pattern amino acids were found within the KSB, distinct from the worldwide consensus of subtype B. Within the KSB, the gag gene sequences from donors O and P and those from the 20 HPs comprised two subclusters. In particular, sequences from donor O strongly clustered with those of eight HPs. Moreover, signature pattern analysis indicated that 14 signature nucleotides were shared between the HPs and LCs within KSB (p < 0.01). Among the 14 nucleotides, positions 9 and 5 belonged to clusters O and P, respectively. In conclusion, signature pattern analysis for the gag gene revealed 12 signature pattern residues within the KSB and also confirmed the previous conclusion that the 20 HPs were infected with viruses due to incompletely inactivated clotting factor IX. This study is the first genetic analysis of the HIV-1 gag gene in Korea.
Highlights
We have previously conducted a nationwide genetic analysis of HIV-1 with sera from individuals in the early stages of infection with HIV-1 with the aim of identifying the cause of an HIV-1 outbreak among hemophiliacs in Korea in 1990–1994
As a result of these molecular epidemiological studies, viruses from two plasma donors, who were paid to donate, were identified as the agents of infection of 20 HIV-1-infected hemophiliacs [1,2,3,4,5]. In these studies [1,2,3,4,5], we conducted in-depth analysis of the pol, vif, env, and nef genes in the Korean subclade of subtype B (KSB) [6,7], but the gag gene is yet to be studied in Korea
We identified 12 signature amino acid residue patterns in the KSB Gag protein that are distinct from worldwide consensus B, and confirmed a previously postulated epidemiological link between the viruses that infected 20 HPs and two plasma donors, in contrast with those that infected local controls (LCs), as shown in previous studies [2,3,4,5]
Summary
We have previously conducted a nationwide genetic analysis of HIV-1 with sera from individuals in the early stages of infection with HIV-1 (before 1994) with the aim of identifying the cause of an HIV-1 outbreak among hemophiliacs in Korea in 1990–1994. As a result of these molecular epidemiological studies, viruses from two plasma donors, who were paid to donate, were identified as the agents of infection of 20 HIV-1-infected hemophiliacs [1,2,3,4,5]. In these studies [1,2,3,4,5], we conducted in-depth analysis of the pol, vif, env, and nef genes in the Korean subclade of subtype B (KSB) [6,7], but the gag gene is yet to be studied in Korea.
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