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

Viruses ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 545 ◽  
Author(s):  
Young-Keol Cho ◽  
Jung-Eun Kim ◽  
Brian T. Foley
Keyword(s):  
Genetic Analysis ◽  
Pattern Analysis ◽  
Direct Sequencing ◽  
Factor Ix ◽  
Full Length ◽  
Clotting Factor ◽  
Gene Sequences ◽  
Subtype B ◽  
Signature Pattern ◽  
Hiv 1

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.

Sequence Length of HIV-1 Subtype B Increases Over Time: Analyzing a Cohort of Patients with Hemophilia Over 30 Years

2021 ◽  
Author(s):  
Young-Keol Cho ◽  
Jung-eun Kim ◽  
Brian Foley
Keyword(s):  
Direct Sequencing ◽  
National Laboratory ◽  
Sequence Length ◽  
Coding Region ◽  
Los Alamos National Laboratory ◽  
Subtype B ◽  
Combined Antiretroviral Therapy ◽  
Signature Pattern ◽  
Hiv 1 ◽  
Over Time

The objective of this study is to investigate whether the sequence length of HIV-1 increases over time. A longitudinal analysis of full-length coding region sequences (FLs) in an outbreak of HIV-1 infection among patients with hemophilia and local controls identified as infected with the Korean subclade B of HIV-1 (KSB). Genes amplified by overlapping RT-PCR or nested PCR were subjected to direct sequencing. In total, 141 FLs were sequentially determined over 30 years in 62 KSB-infected patients. Non-KSB sequences were retrieved from the Los Alamos National Laboratory HIV Database. Phylogenetic analysis indicated that within KSB, 2 FLs from plasma donors O and P comprised two clusters together with 8 and 12 patients with hemophilia, respectively. Signature pattern analysis for the KSB of HIV-1 revealed signature nucleotide residues at 1.05%, compared with local controls. Additionally, in-depth FLs sequence analysis over 30 years in KSB indicates that the KSB FL significantly increases over time before combined antiretroviral therapy (cART) and decreases on cART. Furthermore, the increase in FLs over time significantly occurred in the subtypes B, C and G, but, there was no increase in the subtypes D, A, and F1. Consequently, subtypes F1 and D had the shortest sequence length. Our analysis was extended to compare HIV-1 with HIV-2 and SIVs. Essentially, the longer the sequence length (SIVsm &gt; HIV-2 &gt; SIVcpz &gt; HIV-1), the longer the survival period. The increase in the length of the HIV-1 sequence over time suggests that it might be an evolutionary direction toward attenuated pathogenicity.

Characterization and signature pattern analysis of Korean clade HIV-1 using nef gene sequences

2008 ◽  
Vol 46 (1) ◽  
pp. 88-94 ◽  
Author(s):  
Chan Seung Park ◽  
Dong Hun Lee ◽  
Keon Myung Lee ◽  
Chan-Hee Lee
Keyword(s):  
Pattern Analysis ◽  
Gene Sequences ◽  
Signature Pattern ◽  
Hiv 1

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 ◽  
Vol 53 (6) ◽  
pp. 789-796 ◽  
Author(s):  
Young-Keol Cho ◽  
Jung-Eun Kim ◽  
Daeun Jeong ◽  
Brian T. Foley
Keyword(s):  
Pattern Analysis ◽  
Full Length ◽  
Signature Pattern ◽  
Hiv 1

scholarly journals Sequence Length of HIV-1 Subtype B Increases over Time: Analysis of a Cohort of Patients with Hemophilia over 30 Years

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 806
Author(s):  
Young-Keol Cho ◽  
Jung-Eun Kim ◽  
Brian T. Foley
Keyword(s):  
Direct Sequencing ◽  
Sequence Length ◽  
Coding Region ◽  
Rt Pcr ◽  
Time Analysis ◽  
Variable Regions ◽  
Subtype B ◽  
Signature Pattern ◽  
Hiv 1 ◽  
Over Time

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.

scholarly journals Sequence Length of HIV-1 Subtype B Increases Over Time: Analysis of a Cohort of Patients With Hemophilia Over 30 Years

2021 ◽  
Author(s):  
Young-Keol Cho ◽  
Jung-Eun Kim ◽  
Brian Foley
Keyword(s):  
Direct Sequencing ◽  
Sequence Length ◽  
Coding Region ◽  
Rt Pcr ◽  
Variable Regions ◽  
Subtype B ◽  
Combined Antiretroviral Therapy ◽  
Signature Pattern ◽  
Hiv 1 ◽  
Over Time

We aimed to investigate whether the sequence length of HIV-1 increases over time. A longitudinal analysis of full-length coding region sequences (FLs) during an HIV-1 outbreak among pa-tients with hemophilia and local controls infected with the Korean subclade B of HIV-1 (KSB) was performed. 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 for the KSB of HIV-1 revealed 91 signature nucleotide residues (1.05%). In total, 48 and 43 signature nucleotides originated from clusters O and P, respectively. Only six positions contained 100% specific nucleotide(s) in clusters O and P. Additionally, in-depth FL analysis over 30 years indicates that the KSB FL significantly increased over time before combined antiretroviral therapy (cART) and decreased with cART. The increase occurred due to a significant increase in env and nef genes, originating in the variable regions of both genes. The increase in the sequence length of HIV-1 over time suggests that it has an evolutionary direction.

Tracing the origin and history of HIV-1 subtype B′ epidemic by near full-length genome analyses

AIDS ◽  
2012 ◽  
Vol 26 (7) ◽  
pp. 877-884 ◽  
Author(s):  
Zhe Li ◽  
Xiang He ◽  
Zhe Wang ◽  
Hui Xing ◽  
Fan Li ◽  
...  
Keyword(s):  
Full Length ◽  
Subtype B ◽  
History Of ◽  
Genome Analyses ◽  
Full Length Genome ◽  
Hiv 1

scholarly journals Characterization of HIV-1 near Full-Length Proviral Genome Quasispecies from Patients with Undetectable Viral Load Undergoing First-Line HAART Therapy

2017 ◽  
Author(s):  
Brunna M. Alves ◽  
Juliana D. Siqueira ◽  
Marianne M. Garrido ◽  
Ornella M. Botelho ◽  
Isabel M. Prellwitz ◽  
...  
Keyword(s):  
Viral Load ◽  
Highly Active Antiretroviral Therapy ◽  
Treatment Success ◽  
Undetectable Viral Load ◽  
Hiv Treatment ◽  
Full Length ◽  
Resistance Mutations ◽  
First Line ◽  
Subtype B ◽  
Hiv 1

Increased access to highly active antiretroviral therapy (HAART) by HIV+ individuals has become a reality worldwide. In Brazil, ART currently reaches over half of the HIV-infected subjects. In the context of a remarkable HIV-1 genetic variability, highly related variants, called quasispecies, are generated. HIV quasispecies generated during infection can influence virus persistence and pathogenicity, representing a challenge to treatment. However, the clinical relevance of minority quasispecies is still uncertain. For this study, we have determined the archived proviral sequences, viral subtype and drug resistance mutations from a cohort of HIV+ patients with undetectable viral load undergoing HAART as first-line therapy using next-generation sequencing for near full-length virus genome (NFLG) assembly. HIV-1 consensus sequences representing NFLG were obtained for eleven patients, while for another twelve varying genome coverage rates were obtained. Phylogenetic analysis showed the predominance of subtype B (83%; 19/23). Considering the minority variants, 18 patients carried archived virus harboring at least one mutation conferring antiretroviral resistance; for six patients, the mutations correlated with the current ARVs used. These data highlight the importance of monitoring HIV minority drug resistant variants and their clinical impact, to guide future regimen switches and improve HIV treatment success.

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