Identification of New Subtype of Human Immunodeficiency Virus Type 1 in a Korean Patient

Kim, Nam Joong; Lee, Sun Hee; Park, Sang Won; Choi, Hee Jung; Kim, Thoma; Choi, Jeong Yun; Kim, Jin Wook; Kim, Ui Seok; Gao, Feng; Oh, Myoung Don; Choe, Kang Won

Abstract

BACKGROUD: In the previous study, we determined subtypes of Human Immunodeficiency Virus type 1 (HIV-1) in Korean patients by partial sequence analysis. We showed that eighteen of the nineteen sequences of HIV-1 from Korean fell into subtype B and one fell into subtype A. At that study, HIV-1 identified as subtype A showed 40% diversity from reference sequences and presumed to be a variant of subtype A. The aim of present study is to determine the molecuar biological characteristics of HIV-1 previously identified as subtype A. METHODS: Growth curve was determined. SI/NSI phenotype was determined using a cocultivation assay using MT-2 cells. A complete genome sequence was obtained by amplifying overlapping PCR fragments. Cowork was done to identify the subtype of HIV-1 previously identified as variant A from Korea (97KR004), Cyprus (94CY017), Democratic Republic of Congo (97CDKTB48, 97CDKFE4, 97CDKS10, 97CDKP58). Phylogenetic analysis, distance analysis, diversity plot analysis, bootstrap anlysis were done to identify the subtype of these newly characterized strains. RESULTS: We found that 97KR004 was SI phenotype. Complete sequence of 97KR004 was determined (AF286239). Phylogenetic analysis showed that the four newly characterized strains (94CY017, 97CDKTB48, 97CDKFE4, 97CDKS10) were closely related to subtype A. Subtype distance tool showed that these four strains fell to sub-subtype A2. Diversity plot analysis and bootstrap analysis were done to identify subtype of 97KR004. Nine subtype reference strains and 94CY017 strain were used as reference sequences. These analyses confirmed that 97KR004 represented sub-subtype A2/subtype D recombinant. CONCLUSOIN: We showed that 97KR004 fell into newly identified sub-subtype A2.