Phylogenetic Analysis of Near Full-Length HIV Type 1 Genomic Sequences from 21 Korean Individuals

Abstract

The Korean subclade of subtype B (KSB) is the most prevalent HIV-1 strain found in Korea. To date, only two near full-length HIV-1 sequences from Korean patients have been reported. Here, we analyzed a total of 24 near full-length genomes of HIV-1 strains that were isolated from 17 antiretroviral therapy (ART)-naive patients and four ART-exposed patients. Proviral DNA from peripheral blood mononuclear cells was PCR amplified and directly sequenced. Phylogenetic analyses were used to classify viruses from 19 patients as KSB, from one patient as subtype B, from one patient as subtype D, and three viruses from one patient as CRF02_AG. All KSB viruses demonstrated TAAAA instead of TATAA at the TATA box in the LTR. Of the 19 KSB patients, their sequence identities at the nucleotide level ranged from 89.8% to 97.1% from the lowest env gene to the highest pol gene. Other than the CRF02_AG viruses, no recombination events were noted in any of the 19 KSB patients, which is consistent with our previous studies on the pol, vif, and nef genes. Except for one strain, all of the strains were classified as non-syncytium-inducing strains. This is the first report to describe near full-length KSB.

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

“…In total, 251 HIV-1-infected patients were diagnosed in Korea before 1992. Based on epidemiological data, it appears that 105 patients were domestically infected with KSB, the transmission of which began in 1988 [1,2,13,14], and 40 patients were infected with Western subtype B. There were no samples from about 20 people, and researchers could therefore not determine their HIV-1 subtype.…”

Genetic defects in the nef gene are associated with Korean Red Ginseng intake: monitoring of nef sequence polymorphisms over 20 years

“…In addition, there was a significant inverse correlation found between KRG and the annual decrease of CD4+ T cells and between KRG and RNA copy number in our previous study [22] . Furthermore, we reported that, in addition to clinically beneficial effects, a high frequency of genetic defects, including gΔ nef [5] , [6] , [22] , [23] , [24] , [25] , are associated with the long-term intake of KRG [26] . Consequently, we reported many long-term slow progressors (LTSPs) among a small Korean cohort of HIV-1 patients who have taken KRG for more than 10 yr [26] .…”

“…Furthermore, we reported that, in addition to clinically beneficial effects, a high frequency of genetic defects, including gΔ nef [5] , [6] , [22] , [23] , [24] , [25] , are associated with the long-term intake of KRG [26] . Consequently, we reported many long-term slow progressors (LTSPs) among a small Korean cohort of HIV-1 patients who have taken KRG for more than 10 yr [26] . Among the LTSPs, two patients have remained healthy for 26 yr after diagnosis in the absence of ART [26] , [27] .…”

“…Consequently, we reported many long-term slow progressors (LTSPs) among a small Korean cohort of HIV-1 patients who have taken KRG for more than 10 yr [26] . Among the LTSPs, two patients have remained healthy for 26 yr after diagnosis in the absence of ART [26] , [27] . In the literature, Patient 87-05 might be the longest follow-up case in the absence of ART.…”

Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses

“…A total of 100 HIV-1 subtype B genomes and 50 HIV-1 non-subtype B genomes were randomly pulled (with no duplicates) from the Los Alamos HIV Database (LANL; ) reference genome 2017 list ( Table S1 ; [ 16 , 28 , 40 , 74 , 75 , 76 , 77 , 78 , 79 , 80 , 81 , 82 , 83 , 84 , 85 , 86 , 87 , 88 , 89 , 90 , 91 , 92 , 93 , 94 , 95 , 96 , 97 , 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 , 106 , 107 , 108 , 109 , 110 , 111 , 112 , 113 , 114 , 115 , 116 , 117 , 118 , 119 , 120 , 121 , …”