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

Alves, Brunna M.; Siqueira, Juliana D.; Garrido, Marianne M.; Botelho, Ornella M.; Prellwitz, Isabel M.; Ribeiro, Sayonara Rocha; Soares, Esmeralda A.; Soares, Marcelo A.

doi:10.3390/v9120392

Cited by 20 publications

(23 citation statements)

References 109 publications

(138 reference statements)

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“…The two patients are at a higher risk of therapy failure. Characterization of HIV-1 proviral DNA would be helpful in the monitoring of HIV drug resistance variants clinical impact of regimens and treatment success [3]. Characterization of the proviral genome was indicated to have significance in monitoring HIV minority drug resistant variants in Brazil [3].…”

Section: Discussionmentioning

confidence: 99%

“…Characterization of HIV-1 proviral DNA would be helpful in the monitoring of HIV drug resistance variants clinical impact of regimens and treatment success [3]. Characterization of the proviral genome was indicated to have significance in monitoring HIV minority drug resistant variants in Brazil [3]. Although our samples are limited to nine numbers, genotyping test may be giving valuable information which would be helpful for HIV drug resistant variants in the region of the northern part of India.…”

Section: Discussionmentioning

confidence: 99%

“…The list of mutations provided by the expert groups highlighted the pattern of mutations with drug panels [2]. The full-length HIV-1 proviral genome was characterized [3]. HIV proviral DNA drug resistance mutations were reported from the community treatment program [4].Drug resistance mutation analysis of archived DNA could help in choosing the proper regimen at a low level or suppressed viremia patients [5].Viral Epidemiological Signature Pattern Analysis (VESPA) was used to determine the signature pattern of amino acids and nucleic acid sequences.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of drug resistance mutation and signature pattern in the archived DNA of HIV-1 infected North Indian patients

et al. 2020

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Background Characterization of drug resistance mutations and signature pattern in the archived DNA of HIV-1 infected North Indian patients.Methods Blood samples were collected from 9 patients enrolled in ART Centre, S.N. Medical College, Agra, North India from 1 year to = < 7 years. DNA was isolated and amplified for protease and reverse transcriptase genes using nested primers from WHO dried blood spot protocol 2010. The polymerase chain reaction products were sequenced and drug resistance mutation patterns were analysed using the HIV drug resistance database, Stanford University, USA. Various computational tools and websites like Stanford HIV drug resistance database, Viral epidemiological signature pattern analysis (VESPA), Hypermutation, SNAP version 2.1.1, Entropy were utilized for analysis of the sequence data.Results This study enables an analysis of archived DNA samples in patients having lower viral load and where the situation of HIV RNA isolation was negligible. Lamivudine associated drug-resistant mutations such as M184V/M184I, nevirapine associated mutations Y181C and H221Y and efavirenz associated mutations M230I were observed in two patients. No mutations were observed in the remaining seven patients. The signature pattern analysis of 9 protease and reverse transcriptase genes identified the conservation of amino acid sequences as compared to the reference sequence. The signature pattern of nucleotide substitution (synonymous to non-synonymous ratio) of the protease gene was 5.02 and the reverse transcriptase gene was 7.01. No hyper mutation was observed in the protease and reverse transcriptase gene of the archived DNA.Conclusions The analysis of the drug resistance mutation in the protease and reverse transcriptase gene of the archived DNA of HIV-1 subtype C infected patients over 1 to = < 7 years of first-line ART may be helpful in the treatment guideline in North Indian patients. A few signature amino acids were persisted in the reverse transcriptase and protease gene of similar HIV-1 subtype C infected patients over 1 to = < 7 years of first line ART in comparison to the reference sequence. This archived DNA drug resistance mutation testing could be an important tool when RNA testing becomes unsuccessful.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Analysis of drug resistance mutation and signature pattern in the archived DNA of HIV-1 infected North Indian patients

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“…We used the method already published [29,30] analysis [31]. The study was carried out using only the Pol RT part region of the sequences obtained.…”

Section: Ngs Of Hiv Proviral Dnamentioning

confidence: 99%

Phylogenetic analysis of HIV-1 archived DNA in blood and gut-associated lymphoid tissue in patients receiving antiretroviral therapy: a study from Provir/Latitude45 project

Recordon-Pinson

Tumiotto

Bellecave

et al. 2020

Preprint

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One of the approaches to cure HIV is the use of therapeutic vaccination. We have launched the Provir/Latitude 45 study to identify conserved CTL epitopes in archived HIV-1 DNA according to the HLA class I alleles in aviremic patients under antiretroviral therapy (ART). A HIV-1 polypeptidic therapeutic vaccine based on viral sequence data obtained from circulating blood was proposed; here, our aim was to compare the proviral DNA in blood and gutassociated lymphoid tissue (GALT) at two different levels : nucleotide sequences and potential CTL epitopes. The reverse transcriptase was sequenced in both compartments using next generation sequencing (NGS) in samples from nine individuals, two of which had also single genome sequencing (SGS) performed; phylogenetic trees were established and compared ; CTL epitopes were also identified according to their potential affinity for the HLA alleles .The proviral sequences of both compartments intra-patient exhibited a very low genetic divergence while it was possible to differentiate the sequences inter-patients; SGS analysis of two couples of samples confirmed that there was not a compartmentalization of the sequences intra-patient.When we simulated the CTL epitopes which can be presented by the corresponding HLA alleles in both compartments, no significant difference was observed. We conclude that the proviral DNA sequences in blood and GALT are similar and that the epitope analysis in blood can be considered as relevant to that observed in the GALT, a hard-to-reach major compartment, and can therefore be used for therapeutic vaccine approaches. KeywordsHIV-1, proviral DNA, blood, gut associated lymphoid tissue (GALT), CTL epitopes, phylogenetic comparison of archived viral sequences

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“…Recently, Ji et al [ 10 ] recommended best practices for processing HIV NGS data, which include reference-based assembly using Bowtie2 [ 11 ] as the short read aligner and HXB2 (NCBI accession: K03455; [ 12 ]) as the reference sequence for constructing a consensus sequence. Many studies implement reference-based assembly [ 10 , 13 , 14 ] with tools such as CLC Main Workbench (Qiagen, Hilden, Germany) [ 15 , 16 , 17 , 18 ], Geneious ( ) [ 19 , 20 , 21 , 22 , 23 , 24 ], HyDRA [ 25 , 26 , 27 , 28 ], SmartGene (Switzerland) [ 21 , 29 , 30 ], PAseq [ 31 , 32 ] and Amplicon Variant Analyzer (AVA; pyrosequencing-based platform) [ 21 , 33 , 34 , 35 , 36 , 37 ]. Other studies complete de novo assembly with tools such as Geneious [ 38 ], CLC Main Workbench (Qiagen) [ 16 , 39 , 40 ], and Iterative Virus Assembler (IVA) [ 22 , 41 , 42 , 43 , 44 , 45 , 46 , 47 ].…”

Section: Introductionmentioning

confidence: 99%

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

Gibson

Steiner

Rentia

et al. 2020

Viruses

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Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics. In simulated NGS data, HAPHPIPE generated pol consensus sequences significantly closer to the true consensus sequence than those produced by HyDRA and Geneious and performed comparably to Geneious for HIV gp120 sequences. Furthermore, using empirical data from multiple viruses, we demonstrate that HAPHPIPE can analyze larger sequence datasets due to its greater computational speed. Therefore, we contend that HAPHPIPE provides a more user-friendly platform for users with and without bioinformatics experience to implement current best practices for viral NGS assembly than other currently available options.

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

Cited by 20 publications

References 109 publications

Analysis of drug resistance mutation and signature pattern in the archived DNA of HIV-1 infected North Indian patients

Analysis of drug resistance mutation and signature pattern in the archived DNA of HIV-1 infected North Indian patients

Phylogenetic analysis of HIV-1 archived DNA in blood and gut-associated lymphoid tissue in patients receiving antiretroviral therapy: a study from Provir/Latitude45 project

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

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