scholarly journals Application of next generation sequencing in dual HIV infection studies

2022 ◽  
Vol 98 (6) ◽  
pp. 627-638
Author(s):  
I. A. Lapovok ◽  
P. B. Baryshev ◽  
D. V. Saleeva ◽  
A. A. Kirichenko ◽  
A. V. Shlykova (Murzakova) ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hiv Infection ◽  
Routine Practice ◽  
Next Generation ◽  
Genetic Characteristics ◽  
Synonymous Mutations ◽  
Operational Taxonomic Units ◽  
Subtype B ◽  
Generation Sequencing ◽  
Hiv 1

Introduction. The aim of the study was to use comparative analysis for assessing efficiency of detection and confirmation of dual HIV infection, using conventional population sequencing (PS) and next generation sequencing (NGS) for an HIV-1 pol gene fragment, which encompasses protease and partially reverse transcriptase (positions 2253–3368).Materials and methods. The study was performed on intersubtype dual HIV infection model samples containing viruses of HIV-1 subtype B, sub-subtype A6 and recombinant form CRF63_02A1. Viruses were mixed pairwise in proportions from 10 to 90% to obtain 3 groups of model samples: CRF63vsB, CRF63vsA6, and A6vsB. The nucleotide sequences obtained by using PS and NGS technologies having 5, 10, 15, and 20% sensitivity thresholds for minor virus variants (NGS5–NGS20, respectively) were used to estimate the number of degenerate nucleotides or the degenerate base (DB) count and the number of synonymous mutations (SM) or the SM count. The fragment of the studied region (positions 2725–2981) was used for the analysis of operational taxonomic units.Results. The application of NGS5 proved highly efficient for detection of dual HIV infection in the model samples. The statistically significant (p < 0.01) increase in DB and SM counts was demonstrated by NGS5 compared to PS. As a result, NGS5 helped detect dual HIV infection in 25 out of 27 model samples, while with PS it was detected only in 15 samples. The analysis of operational taxonomic units confirmed dual HIV infection in all the groups of model samples.Discussion. The efficiency of detection and confirmation of dual HIV infection depends both on the content of each virus in the sample and on genetic characteristics of these viruses. Conclusion. Using NGS genetic testing in routine practice will be instrumental for efficient identification of genetic characteristics of infectious agents and for thorough analysis of the epidemiological situation.

scholarly journals A Pan-HIV Strategy for Complete Genome Sequencing

2015 ◽  
Vol 54 (4) ◽  
pp. 868-882 ◽  
Author(s):  
Michael G. Berg ◽  
Julie Yamaguchi ◽  
Elodie Alessandri-Gradt ◽  
Robert W. Tell ◽  
Jean-Christophe Plantier ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Rna Virus ◽  
Consensus Sequence ◽  
Sample Type ◽  
Full Genome ◽  
Next Generation ◽  
Viral Loads ◽  
Subtype B ◽  
Generation Sequencing ◽  
Hiv 1

Molecular surveillance is essential to monitor HIV diversity and track emerging strains. We have developed a universal library preparation method (HIV-SMART [i.e.,switchingmechanismat 5′ end ofRNAtranscript]) for next-generation sequencing that harnesses the specificity of HIV-directed priming to enable full genome characterization of all HIV-1 groups (M, N, O, and P) and HIV-2. Broad application of the HIV-SMART approach was demonstrated using a panel of diverse cell-cultured virus isolates. HIV-1 non-subtype B-infected clinical specimens from Cameroon were then used to optimize the protocol to sequence directly from plasma. When multiplexing 8 or more libraries per MiSeq run, full genome coverage at a median ∼2,000× depth was routinely obtained for either sample type. The method reproducibly generated the same consensus sequence, consistently identified viral sequence heterogeneity present in specimens, and at viral loads of ≤4.5 log copies/ml yielded sufficient coverage to permit strain classification. HIV-SMART provides an unparalleled opportunity to identify diverse HIV strains in patient specimens and to determine phylogenetic classification based on the entire viral genome. Easily adapted to sequence any RNA virus, this technology illustrates the utility of next-generation sequencing (NGS) for viral characterization and surveillance.

Dates of HIV infection can be estimated for seroprevalent patients by coalescent analysis of serial next-generation sequencing data

AIDS ◽  
2011 ◽  
Vol 25 (16) ◽  
pp. 2019-2026 ◽  
Author(s):  
Art F.Y. Poon ◽  
Rachel A. McGovern ◽  
Theresa Mo ◽  
David J.H.F. Knapp ◽  
Bluma Brenner ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Hiv Infection ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Coalescent Analysis ◽  
Generation Sequencing

scholarly journals Universal Amplification, Next-Generation Sequencing, and Assembly of HIV-1 Genomes

2012 ◽  
Vol 50 (12) ◽  
pp. 3838-3844 ◽  
Author(s):  
A. Gall ◽  
B. Ferns ◽  
C. Morris ◽  
S. Watson ◽  
M. Cotten ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Generation Sequencing ◽  
Hiv 1

Routine drug resistance testing in HIV-1 proviral DNA, using an automated next- generation sequencing assay

2019 ◽  
Vol 121 ◽  
pp. 104207 ◽  
Author(s):  
Enagnon Kazali Alidjinou ◽  
Pauline Coulon ◽  
Christophe Hallaert ◽  
Olivier Robineau ◽  
Agnès Meybeck ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Resistance Testing ◽  
Next Generation ◽  
Proviral Dna ◽  
Drug Resistance Testing ◽  
Generation Sequencing ◽  
Hiv 1

scholarly journals Next generation sequencing of HIV-1 protease in the PIVOT trial of protease inhibitor monotherapy

2018 ◽  
Vol 101 ◽  
pp. 63-65 ◽  
Author(s):  
David T. Dunn ◽  
Wolfgang Stöhr ◽  
Alejandro Arenas-Pinto ◽  
Anna Tostevin ◽  
Jean L. Mbisa ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Protease Inhibitor ◽  
Next Generation ◽  
Protease Inhibitor Monotherapy ◽  
Generation Sequencing ◽  
Hiv 1

scholarly journals Mutational profiling in suspected triple-negative essential thrombocythaemia using targeted next-generation sequencing in a real-world cohort

2020 ◽  
pp. jclinpath-2020-206570
Author(s):  
Olga Michail ◽  
Patrick McCallion ◽  
Julie McGimpsey ◽  
Andrew Hindley ◽  
Graeme Greenfield ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Real World ◽  
Triple Negative ◽  
Bone Marrow Examination ◽  
Driver Mutations ◽  
Routine Practice ◽  
Essential Thrombocythaemia ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Generation Sequencing

Essential thrombocythaemia (ET) is driven by somatic mutations involving the JAK2, CALR and MPL genes. Approximately 10% of patients lack driver mutations and are referred as ‘triple-negative’ ET (TN-ET). The diagnosis of TN-ET, however, relies on bone marrow examination that is not always performed in routine practice, and thus in the real-world setting, there are a group of cases with suspected TN-myeloproliferativeneoplasm.In this real-world cohort, patients with suspected TN-ET were initially rescreened for JAK2, CALR and MPL and then targeted next-generation sequencing (NGS) was applied.The 35 patients with suspected TN-ET had a median age at diagnosis of 43 years (range 16–79) and a follow-up of 10 years (range 2–28). The median platelet count was 758×109/L (range 479–2903). Thrombosis prior to and following diagnosis was noted in 20% and 17% of patients. Six patients were JAK2V617F and two patients were CALR positive on repeat screening. NGS results showed that 24 of 27 patients harboured no mutations. Four mutations were noted in three patients.There was no evidence of clonality for the majority of patients with suspected TN-ET with targeted NGS analysis. Detection of driver mutations in those who were previously screened suggests that regular rescreening is required. This study also questions the diagnosis of TN-ET without the existence of a clonal marker.

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