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Genetic Analysis of the Full-Length gag Gene from the Earliest Korean Subclade B of HIV-1: An Outbreak among Korean Hemophiliacs

1
Department of Microbiology, University of Ulsan College of Medicine, Seoul 05505, Korea
2
HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
*
Author to whom correspondence should be addressed.
Viruses 2019, 11(6), 545; https://doi.org/10.3390/v11060545
Received: 14 May 2019 / Revised: 7 June 2019 / Accepted: 11 June 2019 / Published: 11 June 2019
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. View Full-Text
Keywords: HIV-1 gag gene; Korean subclade of subtype B; phylogenetic analysis; signature pattern; hemophiliacs HIV-1 gag gene; Korean subclade of subtype B; phylogenetic analysis; signature pattern; hemophiliacs
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Cho, Y.-K.; Kim, J.-E.; Foley, B.T. Genetic Analysis of the Full-Length gag Gene from the Earliest Korean Subclade B of HIV-1: An Outbreak among Korean Hemophiliacs. Viruses 2019, 11, 545.

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