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Cho YK, Kim JE, Foley BT. Sequence Length of HIV-1 Subtype B Increases over Time: Analysis of a Cohort of Patients with Hemophilia over 30 Years. Viruses 2021; 13:v13050806. [PMID: 33946221 PMCID: PMC8145643 DOI: 10.3390/v13050806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/25/2021] [Accepted: 04/29/2021] [Indexed: 01/27/2023] Open
Abstract
We aimed to investigate whether the sequence length of HIV-1 increases over time. We performed a longitudinal analysis of full-length coding region sequences (FLs) during an HIV-1 outbreak among patients with hemophilia and local controls infected with the Korean subclade B of HIV-1 (KSB). Genes were amplified by overlapping RT-PCR or nested PCR and subjected to direct sequencing. Overall, 141 FLs were sequentially determined over 30 years in 62 KSB-infected patients. Phylogenetic analysis indicated that within KSB, two FLs from plasma donors O and P comprised two clusters, together with 8 and 12 patients with hemophilia, respectively. Signature pattern analysis of the KSB of HIV-1 revealed 91 signature nucleotide residues (1.1%). In total, 48 and 43 signature nucleotides originated from clusters O and P, respectively. Six positions contained 100% specific nucleotide(s) in clusters O and P. In-depth FL analysis for over 30 years indicated that the KSB FL significantly increased over time before combination antiretroviral therapy (cART) and decreased with cART. This increase occurred due to the significant increase in env and nef genes, originating in the variable regions of both genes. The increase in sequence length of HIV-1 over time suggests an evolutionary direction.
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Affiliation(s)
- Young-Keol Cho
- Department of Microbiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
- Correspondence: ; Tel.: +82-2-3010-4283; Fax: +82-2-3010-4259
| | - Jung-Eun Kim
- Department of Microbiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
| | - Brian T. Foley
- HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544, USA;
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Cho YK, Kim JE, Foley BT. 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:v11060545. [PMID: 31212650 PMCID: PMC6631484 DOI: 10.3390/v11060545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/07/2019] [Accepted: 06/11/2019] [Indexed: 01/14/2023] Open
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.
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Affiliation(s)
- Young-Keol Cho
- Department of Microbiology, University of Ulsan College of Medicine, Seoul 05505, Korea.
| | - Jung-Eun Kim
- Department of Microbiology, University of Ulsan College of Medicine, Seoul 05505, Korea.
| | - Brian T Foley
- HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87544, USA.
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Cho YK, Kim JE, Lee SH, Foley BT, Choi BS. Impact of HIV-1 subtype and Korean Red Ginseng on AIDS progression: comparison of subtype B and subtype D. J Ginseng Res 2018; 43:312-318. [PMID: 30976169 PMCID: PMC6437552 DOI: 10.1016/j.jgr.2018.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/11/2018] [Accepted: 07/16/2018] [Indexed: 11/18/2022] Open
Abstract
Background To date, no study has described disease progression in Asian patients infected with HIV-1 subtype D. Methods To determine whether the disease progression differs in patients infected with subtypes D and B prior to starting combination antiretroviral therapy, the annual decline (AD) in CD4+ T cell counts over 96 ± 59 months was retrospectively analyzed in 163 patients and compared in subtypes D and B based on the nef gene. Results CD4+ T cell AD was significantly higher in the six subtype D–infected patients than in the 157 subtype B–infected patients irrespective of Korean Red Ginseng (KRG) treatment (p < 0.001). Of these, two subtype D–infected patients and 116 subtype B–infected patients had taken KRG. AD was significantly lower in patient in the KRG-treated group than in those in the KRG-naïve group irrespective of subtype (p < 0.05). To control for the effect of KRG, patients not treated with KRG were analyzed, with AD found to be significantly greater in subtype D–infected patients than in subtype B–infected patients (p < 0.01). KRG treatment had a greater effect on AD in subtype D–infected patients than in subtype B–infected patients (4.5-fold vs. 1.6-fold). Mortality rates were significantly higher in both the 45 KRG-naïve (p < 0.001) and all 163 (p < 0.01) patients infected with subtype D than subtype B. Conclusion Subtype D infection is associated with a >2-fold higher risk of death and a 2.9-fold greater rate of progression than subtype B, regardless of KRG treatment.
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Affiliation(s)
- Young-Keol Cho
- Department of Microbiology, University of Ulsan College of Medicine, Seoul, Republic of Korea
- Corresponding author. Department of Microbiology, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Republic of Korea.
| | - Jung-Eun Kim
- Department of Microbiology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sun-Hee Lee
- Division of Infectious Diseases, Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
| | - Brian T. Foley
- HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Byeong-Sun Choi
- Division of AIDS, Center for Immunology and Pathology, Korea National Institute of Health, Chung-buk, Republic of Korea
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Cho YK, Kim JE, Foley BT. High Prevalence of Non-B HIV-1 Subtypes in Overseas Sailors and Prostitutes in Korea. AIDS Res Hum Retroviruses 2018; 34:347-353. [PMID: 29334757 DOI: 10.1089/aid.2017.0238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
There have been no studies related to groups at the highest risk for HIV-1 infection in Korea before 1993. In this study, for the first time, we report the distribution of HIV subtypes in overseas sailors (OSs) and prostitutes who worked in brothels near U.S. military bases in Korea. We retrospectively determined the sequences of nef in 131 patients using reverse transcription polymerase chain reaction (RT-PCR). These patients composed of 102 OSs, 14 OS spouses, and 15 prostitutes. Phylogenetic analysis was performed using 128 Korean OSs, OS spouses, and prostitutes. The distribution of non-B subtypes (n = 105) was as follows: 39, CRF02_AG; 15, CRF01_AE; 7, A1; 7, A2; 6, D; 2, CRF06_cpx; 3, C; 6, G; 11, untypable; and 1 each for CRF09_cpx, CRF12_BF, CRF50_A1D, A3, AFG, H, F1, F2, and A. Of the 116 OSs and OS spouses, 101 (87%), 11 (9%), and 4 (3%) subjects had non-B, Western B, and Korean subclade B (KSB) HIV-1s, respectively. Among the 15 prostitutes, 10 had Western B (67%), 4 non-B (27%), and 1 KSB (7%) HIV-1s. All 14 couples, each comprising of an OS and his spouse, had the same subtype. KSB (5%) was detected in OSs and prostitutes in 1990 and 1994, respectively. Of the 131 patients analyzed in this study, 105 (80%), 21 (16%), and 5 (4%) were infected with the non-B, Western B, and KSB subtypes of HIV, respectively. In future, these data may provide an important foundation for analysis of HIV-1 subtypes in Korea.
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Affiliation(s)
- Young-Keol Cho
- Department of Microbiology, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jung-Eun Kim
- Department of Microbiology, University of Ulsan College of Medicine, Seoul, South Korea
| | - Brian T. Foley
- HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
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Cho YK, Kim JE, Jeong D, Foley BT. Signature pattern analysis for the full-length env gene of the earliest Korean subclade B of HIV-1: outbreak among Korean hemophiliacs. Virus Genes 2017. [PMID: 28639219 DOI: 10.1007/s11262-017-1477-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The epidemiological link in the hypervariable env gene between viruses infecting HIV-positive hemophiliacs (HPs) and plasma donors was not studied. We determined full-length env gene sequences in 20 HPs, 3 plasma donors whose plasma was used for domestic clotting factor (DCF) production, and 54 local controls (LCs). Env genes from viruses in frozen stored sera obtained 1-3 years after diagnosis and from samples collected several years after infection were amplified via RT-PCR and subjected to direct sequencing. Phylogenetic analysis indicated that all sequences were subtype B, including 133 sequences from 77 cases (20 HPs, 3 plasma donors, and 54 LCs) belonging to the Korean subclade B (KSB) and 6 sequences from 5 cases that did not belong to the KSB. Env gene sequences from donors O and P and those of the 20 HPs comprised 2 subclusters within the KSB, although phylogenetic analysis did not support significant bootstrap values. In contrast, signature pattern analysis indicated signature nucleotides at 43 positions between the HPs and LCs (P < 0.05). In particular, specific signature nucleotides at 4 positions were fully conserved in the HPs, but not in the LCs (P < 0.0001). Furthermore, there were 26 signature residues within the KSB and were distinct from the worldwide consensus for subtype B. In conclusion, signature pattern analysis for the hypervariable env gene revealed an epidemiological link that the 20 HPs in this study had been infected with viruses from the DCF used for treatment, consistent with our previous finding.
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Affiliation(s)
- Young-Keol Cho
- Department of Microbiology, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, South Korea.
| | - Jung-Eun Kim
- Department of Microbiology, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Daeun Jeong
- Department of Microbiology, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Brian T Foley
- HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
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Abstract
During the evolution of human immunodeficiency virus (HIV), transmissions between humans and primates resulted in multiple HIV lineages in humans. This evolution has been rapid, giving rise to a complex classification and allowing for worldwide spread and intermixing of subtypes, which has consequently led to dozens of circulating recombinant forms. In the Republic of Korea, 12,522 cases of HIV infection have been reported between 1985, when AIDS was first identified, and 2015. This review focuses on the evolution of HIV infection worldwide and the molecular epidemiologic characteristics of HIV in Korea.
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Affiliation(s)
- Bum Sik Chin
- Center for Infectious Diseases, National Medical Center, Seoul, Korea.
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Cho YK, Kim JE, Woo JH. Genetic defects in the nef gene are associated with Korean Red Ginseng intake: monitoring of nef sequence polymorphisms over 20 years. J Ginseng Res 2016; 41:144-150. [PMID: 28413318 PMCID: PMC5386103 DOI: 10.1016/j.jgr.2016.02.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/19/2016] [Accepted: 02/19/2016] [Indexed: 01/11/2023] Open
Abstract
Background The presence of gross deletions in the human immunodeficiency virus nef gene (gΔnef) is associated with long-term nonprogression of infected patients. Here, we investigated how quickly genetic defects in the nef gene are associated with Korean Red Ginseng (KRG) intake in 10 long-term slow progressors. Methods This study was divided into three phases over a 20-yr period; baseline, KRG intake alone, and KRG plus highly active antiretroviral therapy (ART). nef gene amplicons were obtained using reverse transcription polymerase chain reaction (PCR) and nested PCR from 10 long-term slow progressors (n = 1,396), and nested PCR from 36 control patients (n = 198), and 28 ART patients (n = 157), and these were then sequenced. The proportion of gΔnef, premature stop codons, and not in-frame insertion or deletion of a nucleotide was compared between three phases, control, and ART patients. Results The proportion of defective nef genes was significantly higher in on-KRG patients (15.6%) than in baseline (5.7%), control (5.6%), on-KRG plus ART phase (7.8%), and on-ART patients (6.6%; p < 0.01). Small in-frame deletions or insertions were significantly more frequent among patients treated with KRG alone compared with controls (p < 0.01). Significantly fewer instances of genetic defects were detected in samples taken during the KRG plus ART phase (7.8%; p < 0.01). The earliest defects detected were gΔnef and small in-frame deletions after 7 mo and 67 mo of KRG intake, respectively. Conclusion KRG treatment might induce genetic defects in the nef gene. This report provides new insight into the importance of genetic defects in the pathogenesis of AIDS.
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Affiliation(s)
- Young-Keol Cho
- Department of Microbiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jung-Eun Kim
- Department of Microbiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jun-Hee Woo
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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Kim BR, Kim JE, Sung H, Cho YK. Long-term follow up of HIV-1-infected Korean haemophiliacs, after infection from a common source of virus. Haemophilia 2015; 21:e1-11. [PMID: 25545303 DOI: 10.1111/hae.12527] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2014] [Indexed: 12/21/2022]
Abstract
In the early 1990s, 20 haemophiliacs (HPs) were infected with a common source of HIV-1 viruses through the contaminated clotting factor IX. The aim of this study is to review 20 HPs infected with a common source of virus. The enrolled patients have been consecutively treated with Korean red ginseng (KRG), zidovudine (ZDV) or two-drug therapy and highly active antiretroviral therapy (HAART). We determined full-length pol gene over 20 years and human leukocyte antigen (HLA) class I with peripheral blood mononuclear cells and reviewed medical records. Eighteen HPs experienced various opportunistic infections or clinical manifestations. There were significant inverse correlations between the HLA prognostic score and the annual decrease in CD4+ T-cell counts prior to HAART (AD) (P < 0.05) and the amount of KRG and the AD (P < 0.01). From 1998, the HPs had been treated with HAART. Each of the two patients died without and with HAART regimen respectively. At present, 16 HPs have been alive with HAART. Among the 16 HPs, 12 and 4 are on HAART-plus-KRG and HAART only respectively. Eleven HPs including 2 HPs with G-to-A hypermutations had revealed resistance mutations. Ten and two HPs have shown poor adherence and incomplete viral suppres-sion on HAART respectively. Virological failure based on WHO guidelines was not observed on KRG-plus-HAART. Two HPs revealed additional resistance mutations against two classes on KRG-plus-HAART. As a nationwide study, we first report overall features on clinical course of Korean haemophiliacs. Further education on the importance of drug adherence is needed.
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Affiliation(s)
- B-R Kim
- Departments of Microbiology; and Department of Laboratory Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
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Cho YK, Kim JE, Foley BT. Phylogenetic analysis of near full-length HIV type 1 genomic sequences from 21 Korean individuals. AIDS Res Hum Retroviruses 2013. [PMID: 23199052 DOI: 10.1089/aid.2012.0298] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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.
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Affiliation(s)
- Young-Keol Cho
- Department of Microbiology, University of Ulsan College of Medicine, Seoul, Korea
| | - Jung-Eun Kim
- Department of Microbiology, University of Ulsan College of Medicine, Seoul, Korea
| | - Brian T. Foley
- HIV Databases, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico
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