Annals of Clinical Microbiology, The official Journal of the Korean Society of Clinical Microbiology


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Indexed in KCI, KoreaMed, Synapse, DOAJ
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pISSN 2288-0585 eISSN 2288-6850

DNA Sequence Analysis of the V3 loop of HIV-1 from Korean Patients with AIDS

Original article

Annals of Clinical Microbiology (Ann Clin Microbiol) 1999 June Volume 2, Issue 1, pages 19-27.

DNA Sequence Analysis of the V3 loop of HIV-1 from Korean Patients with AIDS

Jae Seok Kim, M.D., Sung Sup Park, M.D., Kyou Sup Han, M.D., Eui Chong Kim, M.D., Jin Q Kim, M.D., Myoung Hee Park, M.D. and Han Ik Cho, M.D.

Department of Clinical Pathology, Seoul National University College of Medicine, Seoul, Korea


Background:Phylogenetic analysis was used to determine the subtype and the probable source of transmission of human immunodeficiency virus type 1 (HIV-1). The HIV-1 is an RNA virus characterized by extensive genetic variation. To determine the extent of HIV-1 genetic variation, HIV-1 envelope V3 domain structures were analyzed and compared. In this study, we analyzed phylogenetic relationships and the subtype of Korean isolates to help the epidemiological study of HIV-1 infection.

Methods:Peripheral blood mononuclear cells were collected from eight patients with AIDS. HIV-1 proviral DNA was directly amplified directly by polymerase chain reaction (PCR). V3 domain nucleotide sequences were determined using a direct sequencing method with PCR products. Phylogenetic analysis of V3 domain nucleotide sequences was performed comparing with previously documented HIV-1 strains.

Results:Six V3 loop sequences were obtained from eight HIV-1 infected patients. All of six HIV-1 strains were classified as subtype B by phylogenetic analysis of the V3 region. The distances between strains varied from 11.5% to 22.9% (mean; 15.9%), showing six strains were not related each other.

Conclusions:Six HIV-1 strains belong to subtype B, which is the prevalent type in North America, Europe, and Japan. Molecular epidemiological data supported the transmission of HIV-1 to Korea from these areas. Phylogenetic analysis revealed the absence of closely related strains in these isolates. Direct sequencing of V3 loop DNA would be a useful tool to determine the subgroup and the route of transmission of HIV-1. (Korean J Clin Microbiol 1999;2:19~27)


HIV-1, V3 sequence, Phylogenetic analysis, Molecular epidemiology