Analytical Assessment of the Vela Diagnostics NGS Assay for HIV Genotyping and Resistance Testing: The Apulian Experience

Bonifacio, Maria Addolorata; Genchi, C.; Lagioia, Antonella; Talamo, Vincenza; Volpe, Anna; Mariggiò, Maria Addolorata

doi:10.3390/ijms23052727

Cited by 11 publications

(3 citation statements)

References 37 publications

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“…In conclusion, our study complements previous studies [ 23 , 24 , 33 , 46 , 47 , 48 , 49 ] that support the notion that the population sequencing and high-throughput sequencing are well correlated. Moreover, using HTS-GRT, we can detect minority DRMs that have previously been reported to be associated with poor virologic suppression.…”

Section: Discussionsupporting

confidence: 89%

Towards Next-Generation Sequencing for HIV-1 Drug Resistance Testing in a Clinical Setting

Teo

Norhisham

Lee³

et al. 2022

Viruses

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The HIV genotypic resistance test (GRT) is a standard of care for the clinical management of HIV/AIDS patients. In recent decades, population or Sanger sequencing has been the foundation for drug resistance monitoring in clinical settings. However, the advent of high-throughput or next-generation sequencing has caused a paradigm shift towards the detection and characterization of low-abundance covert mutations that would otherwise be missed by population sequencing. This is clinically significant, as these mutations can potentially compromise the efficacy of antiretroviral therapy, causing poor virologic suppression. Therefore, it is important to develop a more sensitive method so as to reliably detect clinically actionable drug-resistant mutations (DRMs). Here, we evaluated the diagnostic performance of a laboratory-developed, high-throughput, sequencing-based GRT using 103 archived clinical samples that were previously tested for drug resistance using population sequencing. As expected, high-throughput sequencing found all the DRMs that were detectable by population sequencing. Significantly, 78 additional DRMs were identified only by high-throughput sequencing, which is statistically significant based on McNemar’s test. Overall, our results complement previous studies, supporting the notion that the two methods are well correlated, and the high-throughput sequencing method appears to be an excellent alternative for drug resistance testing in a clinical setting.

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Section: Discussionsupporting

confidence: 89%

Towards Next-Generation Sequencing for HIV-1 Drug Resistance Testing in a Clinical Setting

Teo

Norhisham

Lee³

et al. 2022

Viruses

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“…A recent Italian study that evaluated the Vela Diagnostics system showed better results with this NGS technology, compared to Sanger sequencing, in terms of the success rate, accuracy, repeatability, and reproducibility of results [21]. Several other studies conducted prior to this Italian study had evaluated and demonstrated the performance of the Vela Dx Sentosa next-generation sequencing system for HIV-1 cDNA genotypic resistance [22][23][24][25].…”

Section: Introductionmentioning

confidence: 85%

Optimization of HIV Sequencing Method Using Vela Sentosa Library on Miseq Ilumina Platform

Papa Mze,

Fernand-Laurent,

Daugabel

et al. 2024

Genes

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Genotypic testing is often recommended to improve the management of patients infected with human immunodeficiency virus (HIV). To help combat this major pandemic, next-generation sequencing (NGS) techniques are widely used to analyse resistance to antiretroviral drugs. In this study, we used a Vela Sentosa kit (Vela Diagnostics, Kendall, Singapore), which is usually used for the Ion Torrent personal genome machine (PGM) platform, to sequence HIV using the Illumina Miseq platform. After RNA extraction and reverse transcriptase-polymerase chain reaction (RT-PCR), minor modifications were applied to the Vela Sentosa kit to adapt it to the Illumina Miseq platform. Analysis of the results showed the same mutations present in the samples using both sequencing platforms. The total number of reads varied from 185,069 to 752,343 and from 642,162 to 2,074,028 in the Ion Torrent PGM platform and the Illumina Miseq platform, respectively. The average depth was 21,955 and 46,856 for Ion Torrent PGM and Illumina Miseq platforms, respectively. The cost of sequencing a run of eight samples was quite similar between the two platforms (about USD 1790 for Illumina Miseq and about USD 1833 for Ion Torrent PGM platform). We have shown for the first time that it is possible to adapt and use the Vela Sentosa kit for the Illumina Miseq platform to obtain high-quality results with a similar cost.

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“…A recent Italian study that evaluated the Vela Diagnostics system showed better results with this NGS technology, compared to Sanger sequencing, in terms of success rate, accuracy, repeatability, and reproducibility of results [12]. In the present study, for the first time, we used a Vela Sentosa kit to sequence HIV genomes using the Illumina Miseq platform.…”

Section: Introductionmentioning

confidence: 87%

Optimization of HIV Sequencing Method Using Vela Sentosa Library on Miseq Ilumina Platform

Papa Mze,

Fernand-Laurent,

Daugabel

et al. 2024

Preprint

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Genotypic testing is often recommended to improve the management of patients infected with human immunodeficiency virus (HIV). To help combat this major pandemic, next-generation sequencing (NGS) techniques are widely used to analyse resistance to antiretroviral drugs. In this study, we used a Vela Sentosa kit, which is usually used for the Ion Torrent personal genome machine (PGM) platform, to sequence HIV using the Illumina Miseq platform. After RNA extraction and reverse transcriptase-polymerase chain reaction (RT-PCR), minor modifications were applied to the Vela Sentosa kit to adapt it to Illumina Miseq platform. Analysis of the results showed the same mutations present in the samples using both sequencing platforms. The total number of reads varied from 185,069 to 752,343 and from 642,162 to 2,074,028 in the Ion Torrent PGM platform and the Illumina Miseq platform, respectively. The average depth was 21955 and 46856 for Ion Torrent PGM and Illumina Miseq platforms, respectively. The cost of sequencing a run of eight samples was closely similar between the two platforms (about 1 790 United States dollars [USD] for Illumina Miseq and about 1833 USD for Ion Torrent PGM platform). We have shown for the first time that it is possible to adapt and use the Vela Sentosa kit for the Illumina Miseq platform to obtain high quality results with a similar cost.

show abstract

Analytical Assessment of the Vela Diagnostics NGS Assay for HIV Genotyping and Resistance Testing: The Apulian Experience

Cited by 11 publications

References 37 publications

Towards Next-Generation Sequencing for HIV-1 Drug Resistance Testing in a Clinical Setting

Towards Next-Generation Sequencing for HIV-1 Drug Resistance Testing in a Clinical Setting

Optimization of HIV Sequencing Method Using Vela Sentosa Library on Miseq Ilumina Platform

Optimization of HIV Sequencing Method Using Vela Sentosa Library on Miseq Ilumina Platform

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