A1 Signature pattern and phylogenetic analysis of full-length env genes in 20 hemophiliacs infected with Korean subclade of HIV-1 subtype B

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.

Download Full-text

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

AIDS ◽

10.1097/qad.0b013e328351430d ◽

2012 ◽

Vol 26 (7) ◽

pp. 877-884 ◽

Cited By ~ 56

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

Download Full-text

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

10.20944/preprints202102.0575.v1 ◽

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 > HIV-2 > SIVcpz > 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.

Download Full-text

Sequencing and Phylogenetic Analysis of Near Full-Length HIV-1 Subtypes A, B, G and Unique Recombinant AC and AD Viral Strains Identified in South Africa

AIDS Research and Human Retroviruses ◽

10.1089/aid.2014.0230 ◽

2015 ◽

Vol 31 (4) ◽

pp. 412-420 ◽

Cited By ~ 6

Author(s):

Eduan Wilkinson ◽

Vera Holzmayer ◽

Graeme B. Jacobs ◽

Tulio de Oliveira ◽

Catherine A. Brennan ◽

...

Keyword(s):

South Africa ◽

Phylogenetic Analysis ◽

Full Length ◽

Hiv 1

Download Full-text

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

10.20944/preprints201712.0024.v1 ◽

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.

Download Full-text

HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing

Viruses ◽

10.3390/v12010063 ◽

2020 ◽

Vol 12 (1) ◽

pp. 63

Author(s):

Lunar ◽

Mlakar ◽

Zorec ◽

Poljak

Keyword(s):

Genome Sequencing ◽

Recombination Event ◽

Patient Management ◽

Full Length ◽

Base Pairs ◽

Comprehensive Collection ◽

Subtype B ◽

Full Length Genome ◽

Hiv 1 ◽

Hiv Diversity

Surveillance of HIV circulating recombinant forms (CRFs) is important because HIV diversity can affect various aspects of HIV infection from prevention to diagnosis and patient management. A comprehensive collection of pol sequences obtained from individuals diagnosed with HIV-1 from 2000 to 2016 in Slovenia was subtyped to identify possible unique recombinant forms (URFs). Selected samples were subjected to near full-length genome (NFLG) sequencing and detailed recombination analyses. Discordant subtyping results were observed for 68/387 (17.6%) sequences and 20 sequences were identified as the most probable URFs and selected for NFLG characterization. Further, 11 NFLGs and two sequences of >7000 base pairs were obtained. Seven sequences were identified as “pure” subtypes or already characterized CRFs: subtype B (n = 5), sub-subtype A6 (n = 1), and CRF01_AE (n = 1). The remaining six sequences were determined to be URFs; four displayed a single recombination event and two exhibited a complex recombination pattern involving several subtypes or CRFs. Finally, three HIV strains were recognized as having epidemic potential and could be further characterized as new CRFs. Our study shows that the identification of new CRFs is possible, even in countries where HIV diversity is considered limited, emphasizing the importance of the surveillance of HIV recombinant forms.

Download Full-text

Construction and characterization of a full-length infectious clone from a fast-replicating, X4-tropic HIV-1 subtype B′ isolate

Archives of Virology ◽

10.1007/s00705-010-0776-z ◽

2010 ◽

Vol 155 (12) ◽

pp. 1923-1931 ◽

Cited By ~ 2

Author(s):

Shou-li Wu ◽

Yan-sheng Yan ◽

Ping-ping Yan ◽

Hai-long Huang ◽

Hui-rong Wang

Keyword(s):

Infectious Clone ◽

Full Length ◽

Subtype B ◽

Hiv 1

Download Full-text

MOLECULAR EPIDEMIOLOGICAL ANALYSIS OF HIV INFECTION IN NORTHERN SEAPORTS OF RUSSIA

Voprosy Virusologii ◽

10.18821/0507-4088-2017-62-4-154-161 ◽

2017 ◽

Vol 62 (4) ◽

pp. 154-161 ◽

Cited By ~ 4

Author(s):

E. V. Kazennova ◽

V. Yu. Laga ◽

K. B. Gromov ◽

M. N. Sankov ◽

E. S. Popova ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Hiv Infection ◽

Central Asia ◽

Epidemiological Analysis ◽

East European ◽

Subtype B ◽

The Common ◽

Former Ussr ◽

Hiv 1 ◽

Regions Of Russia

The results of the molecular-epidemiological analysis of HIV-1 variants circulating in Arkhangelsk and Murmansk - northern seaports of Russia - were presented. In these seaports the HIV-1 variants belonging to subtype A1 were predominant (93% in Murmansk, 83% in Arkhangelsk). In addition to these variants, viruses of other subtypes such as B, C, D and recombinant forms CRF02_AG and CRF03_AB were identified. The heterogeneity of circulating HIV-1 variants was higher in Arkhangelsk than in Murmansk. According to the results of phylogenetic analysis, subtype A1 sequences formed the common branch with nucleotide sequences of IDU-A strains found in other regions of Russia. HIV-1 variants of subtype B sub-clustered with sequences of East European B-variants. The recombinant strains CRF02_AG formed the common branch with HIV-1 sequences from Central Asia republics of the former USSR. Among 124 therapy-naive patients from Arkhangelsk and Murmansk (n = 124) the transmitted resistance was less than 5%.

Download Full-text

Molecular Cloning and Phylogenetic Analysis of Human Immunodeficiency Virus Type 1 Subtype C: a Set of 23 Full-Length Clones from Botswana

Journal of Virology ◽

10.1128/jvi.73.5.4427-4432.1999 ◽

1999 ◽

Vol 73 (5) ◽

pp. 4427-4432 ◽

Cited By ~ 95

Author(s):

Vladimir A. Novitsky ◽

Monty A. Montano ◽

Mary F. McLane ◽

Boris Renjifo ◽

Fredrik Vannberg ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Human Immunodeficiency Virus Type ◽

Virus Type ◽

Southern Africa ◽

Full Length ◽

Subtype C ◽

Subtype B ◽

Immunodeficiency Virus ◽

Hiv 1

ABSTRACT To better understand the virological aspect of the expanding AIDS epidemic in southern Africa, a set of 23 near-full-length clones of human immunodeficiency virus type 1 (HIV-1) representing eight AIDS patients from Botswana were sequenced and analyzed phylogenetically. All study viruses from Botswana belonged to HIV-1 subtype C. The interpatient diversity of the clones from Botswana was higher than among full-length isolates of subtype B or among a set of full-length HIV-1 genomes of subtype C from India (mean value of 9.1% versus 6.5 and 4.3%, respectively; P < 0.0001 for both comparisons). Similar results were observed in all genes across the entire viral genome. We suggest that the high level of HIV-1 diversity might be a typical feature of the subtype C epidemic in southern Africa. The reason or reasons for this diversity are unclear, but may include an altered replication efficiency of HIV-1 subtype C and/or the multiple introduction of different subtype C viruses.

Download Full-text