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

Viruses ◽  
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.

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 recombinant and subtype B near full-length genome among men who have sex with men in South Korea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sangmi Ryou ◽  
Myeongsu Yoo ◽  
Kisoon Kim ◽  
Sangsoo Kim ◽  
Sang Il Kim ◽  
...  
Keyword(s):  
Full Length ◽  
The Novel ◽  
Full Genome Sequencing ◽  
Viral Genomes ◽  
Subtype B ◽  
Predominant Variant ◽  
Sex With Men ◽  
Next Generation Sequencing Ngs ◽  
Full Length Genome ◽  
Hiv 1

AbstractIn Korea, subtype B is the predominant variant of HIV-1, but full genome sequencing and analysis of its viral variants are lacking. We performed near full-length genome (NFLG) sequencing and phylogenetic and recombination analyses of fifty plasma samples from HIV-positive men who have sex with men (MSM) from a Korea HIV/AIDS cohort study. Viral genomes were amplified and the near-full-length sequences were determined using next-generation sequencing (NGS) and Sanger sequencing. We focused on the HIV-1 subtype classification and identification of HIV recombinants. Twelve HIV-1 NFLGs were determined: ten were subtyped as pure HIV-1 subtype B and two recombinant strains as a common subtype CRF07_BC, and a novel subtype CRF43_02G recombined with CRF02_AG again, or a new CRF02_AG and subtype G recombinant. For the ten NFLGs determined by NGS, “the novel recombinant emerged at approximately 2003 and the other nine subtype B about 2004 or 2005”. This is the first report analyzing HIV-1 NFLG, including recombinants and clinical characteristics, by subtype among MSM in Korea. Our results provide novel insights for understanding the recombinants in the HIV-1 epidemic in Korea.

Full-Length Genome Sequencing of HIV Type 1 Group O Viruses Isolated from a Heterosexual Transmission Cluster in Senegal

2001 ◽  
Vol 17 (12) ◽  
pp. 1211-1216 ◽  
Author(s):  
Coumba Toure Kane ◽  
Celine Montavon ◽  
Mama Awa Toure ◽  
Mame Awa Faye ◽  
Aissatou Gueye Ndiaye ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Full Length ◽  
Heterosexual Transmission ◽  
Hiv Type 1 ◽  
Full Length Genome

scholarly journals Near Full-Length Genome Identification of a Novel HIV-1 Recombinant Form (CRF01_AE/B′/C) Among Heterosexuals in Jilin, China

2014 ◽  
Vol 30 (7) ◽  
pp. 695-700 ◽  
Author(s):  
Xingguang Li ◽  
Chuanyi Ning ◽  
Yanli Chen ◽  
Yi Feng ◽  
Min Wei ◽  
...  
Keyword(s):  
Full Length ◽  
Recombinant Form ◽  
Full Length Genome ◽  
Hiv 1

Full-Length Genome Analysis of HIV-1 Subtype C Utilizing CXCR4 and Intersubtype Recombinants Isolated in South Africa

2002 ◽  
Vol 18 (12) ◽  
pp. 879-886 ◽  
Author(s):  
Maria A. Papathanasopoulos ◽  
Tonie Cilliers ◽  
Lynn Morris ◽  
John L. Mokili ◽  
William Dowling ◽  
...  
Keyword(s):  
South Africa ◽  
Genome Analysis ◽  
Full Length ◽  
Subtype C ◽  
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.

Full‐length genome sequencing of RNA viruses—How the approach can enlighten us on hepatitis C and hepatitis E viruses

2020 ◽  
Author(s):  
Elodie Laugel ◽  
Cédric Hartard ◽  
Hélène Jeulin ◽  
Sibel Berger ◽  
Véronique Venard ◽  
...  
Keyword(s):  
Hepatitis C ◽  
Genome Sequencing ◽  
Rna Viruses ◽  
Hepatitis E ◽  
Full Length ◽  
Full Length Genome

scholarly journals Structure-Guided Redesign Increases the Propensity of HIV Env To Generate Highly Stable Soluble Trimers

2015 ◽  
Vol 90 (6) ◽  
pp. 2806-2817 ◽  
Author(s):  
Javier Guenaga ◽  
Viktoriya Dubrovskaya ◽  
Natalia de Val ◽  
Shailendra K. Sharma ◽  
Barbara Carrette ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
Small Animal ◽  
Subtype C ◽  
Disulfide Linkage ◽  
Vaccine Candidates ◽  
Subtype B ◽  
Subtype A ◽  
Induced Changes ◽  
Hiv 1 ◽  
Hiv Diversity

ABSTRACTDue to high viral diversity, an effective HIV-1 vaccine will likely require Envs derived from multiple subtypes to generate broadly neutralizing antibodies (bNAbs). Soluble Env mimics, like the native flexibly linked (NFL) and SOSIP trimers, derived from the subtype A BG505 Env, form homogeneous, stable native-like trimers. However, other Env sequences, such as JRFL and 16055 from subtypes B and C, do so to a lesser degree. The high-resolution BG505 SOSIP crystal structures permit the identification and redesign of Env elements involved in trimer stability. Here, we identified structure trimer-derived (TD) residues that increased the propensity of the subtype B JRFL and subtype C 16055 Env sequences to form well-ordered, homogenous, and highly stable soluble trimers. The generation of these spike mimics no longer required antibody-based selection, positive or negative. Using the redesigned subtype B and C trimer representatives as respective foundations, we further stabilized the NFL TD trimers by engineering an intraprotomer disulfide linkage in the prebridging sheet, I201C-A433C (CC), that locks the gp120 in the receptor nontriggered state. We demonstrated that this disulfide pair prevented CD4 induced-conformational rearrangements in NFL trimers derived from the prototypic subtype A, B, and C representatives. Coupling the TD-based design with the engineered disulfide linkage, CC, increased the propensity of Env to form soluble highly stable spike mimics that are resistant to CD4-induced changes. These advances will allow testing of the hypothesis that such stabilized immunogens will more efficiently elicit neutralizing antibodies in small-animal models and primates.IMPORTANCEHIV-1 displays unprecedented global diversity circulating in the human population. Since the envelope glycoprotein (Env) is the target of neutralizing antibodies, Env-based vaccine candidates that address such diversity are needed. Soluble well-ordered Env mimics, typified by NFL and SOSIP trimers, are attractive vaccine candidates. However, the current designs do not allow most Envs to form well-ordered trimers. Here, we made design modifications to increase the propensity of representatives from two of the major HIV subtypes to form highly stable trimers. This approach should be applicable to other viral Envs, permitting the generation of a repertoire of homogeneous, highly stable trimers. The availability of such an array will allow us to assess if sequential or cocktail immune strategies can overcome some of the vaccine challenges presented by HIV diversity.

scholarly journals Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Chenjie Wan ◽  
◽  
Nadine Bachmann ◽  
Venelin Mitov ◽  
François Blanquart ◽  
...  
Keyword(s):  
Viral Genome ◽  
Genetic Factors ◽  
Significant Fraction ◽  
Genome Sequences ◽  
Subtype B ◽  
Tentative Evidence ◽  
Full Length Genome ◽  
The Impact ◽  
Hiv 1

Abstract The HIV-1 reservoir is the major hurdle to curing HIV-1. However, the impact of the viral genome on the HIV-1 reservoir, i.e. its heritability, remains unknown. We investigate the heritability of the HIV-1 reservoir size and its long-term decay by analyzing the distribution of those traits on viral phylogenies from both partial-pol and viral near full-length genome sequences. We use a unique nationwide cohort of 610 well-characterized HIV-1 subtype-B infected individuals on suppressive ART for a median of 5.4 years. We find that a moderate but significant fraction of the HIV-1 reservoir size 1.5 years after the initiation of ART is explained by genetic factors. At the same time, we find more tentative evidence for the heritability of the long-term HIV-1 reservoir decay. Our findings indicate that viral genetic factors contribute to the HIV-1 reservoir size and hence the infecting HIV-1 strain may affect individual patients’ hurdle towards a cure.

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