HIV-PULSE : a long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization
- Author
- Laurens Lambrechts (UGent) , Noah Bonine (UGent) , Rita Verstraeten (UGent) , Marion Pardons (UGent) , Ytse Noppe (UGent) , Sofie Rutsaert (UGent) , Filip Van Nieuwerburgh (UGent) , Wim Van Criekinge (UGent) , Basiel Cole and Linos Vandekerckhove (UGent)
- Organization
- Project
- Abstract
- A deep understanding of the composition of the HIV-1 reservoir is necessary for the development of targeted therapies and the evaluation of curative efforts. However, current near full-length (NFL) HIV-1 proviral genome sequencing assays are based on labor-intensive and costly principles of repeated PCRs at limiting dilution, restricting their scalability. To address this, we developed a high-throughput, long-read sequencing assay called HIV-PULSE (HIV Proviral UMI-mediated Long-read Sequencing). This assay uses unique molecular identifiers (UMIs) to tag individual HIV-1 genomes, allowing for the omission of the limiting dilution step and enabling long-range PCR amplification of many NFL genomes in a single PCR reaction, while simultaneously overcoming poor single-read accuracy. We optimized the assay using HIV-infected cell lines and then applied it to blood samples from 18 individuals living with HIV on antiretroviral therapy, yielding a total of 1,308 distinct HIV-1 genomes. Benchmarking against the widely applied Full-Length Individual Proviral Sequencing assay revealed similar sensitivity (11% vs 18%) and overall good concordance, though at a significantly higher throughput. In conclusion, HIV-PULSE is a cost-efficient and scalable assay that allows for the characterization of the HIV-1 proviral landscape, making it an attractive method to study the HIV-1 reservoir composition and dynamics.
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Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01GQ7J5A10VWAEX7PBTBHVWB5N
- MLA
- Lambrechts, Laurens, et al. “HIV-PULSE : A Long-Read Sequencing Assay for High-Throughput near Full-Length HIV-1 Proviral Genome Characterization.” BioRXiv, Cold Spring Harbor Laboratory, 2023, doi:10.1101/2023.01.18.524396.
- APA
- Lambrechts, L., Bonine, N., Verstraeten, R., Pardons, M., Noppe, Y., Rutsaert, S., … Vandekerckhove, L. (2023). HIV-PULSE : a long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization. https://doi.org/10.1101/2023.01.18.524396
- Chicago author-date
- Lambrechts, Laurens, Noah Bonine, Rita Verstraeten, Marion Pardons, Ytse Noppe, Sofie Rutsaert, Filip Van Nieuwerburgh, Wim Van Criekinge, Basiel Cole, and Linos Vandekerckhove. 2023. “HIV-PULSE : A Long-Read Sequencing Assay for High-Throughput near Full-Length HIV-1 Proviral Genome Characterization.” BioRXiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.01.18.524396.
- Chicago author-date (all authors)
- Lambrechts, Laurens, Noah Bonine, Rita Verstraeten, Marion Pardons, Ytse Noppe, Sofie Rutsaert, Filip Van Nieuwerburgh, Wim Van Criekinge, Basiel Cole, and Linos Vandekerckhove. 2023. “HIV-PULSE : A Long-Read Sequencing Assay for High-Throughput near Full-Length HIV-1 Proviral Genome Characterization.” BioRXiv. Cold Spring Harbor Laboratory. doi:10.1101/2023.01.18.524396.
- Vancouver
- 1.Lambrechts L, Bonine N, Verstraeten R, Pardons M, Noppe Y, Rutsaert S, et al. HIV-PULSE : a long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization. BioRXiv. Cold Spring Harbor Laboratory; 2023.
- IEEE
- [1]L. Lambrechts et al., “HIV-PULSE : a long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization,” BioRXiv. Cold Spring Harbor Laboratory, 2023.
@misc{01GQ7J5A10VWAEX7PBTBHVWB5N,
abstract = {{A deep understanding of the composition of the HIV-1 reservoir is necessary for the development of targeted therapies and the evaluation of curative efforts. However, current near full-length (NFL) HIV-1 proviral genome sequencing assays are based on labor-intensive and costly principles of repeated PCRs at limiting dilution, restricting their scalability. To address this, we developed a high-throughput, long-read sequencing assay called HIV-PULSE (HIV Proviral UMI-mediated Long-read Sequencing). This assay uses unique molecular identifiers (UMIs) to tag individual HIV-1 genomes, allowing for the omission of the limiting dilution step and enabling long-range PCR amplification of many NFL genomes in a single PCR reaction, while simultaneously overcoming poor single-read accuracy. We optimized the assay using HIV-infected cell lines and then applied it to blood samples from 18 individuals living with HIV on antiretroviral therapy, yielding a total of 1,308 distinct HIV-1 genomes. Benchmarking against the widely applied Full-Length Individual Proviral Sequencing assay revealed similar sensitivity (11% vs 18%) and overall good concordance, though at a significantly higher throughput. In conclusion, HIV-PULSE is a cost-efficient and scalable assay that allows for the characterization of the HIV-1 proviral landscape, making it an attractive method to study the HIV-1 reservoir composition and dynamics.}},
author = {{Lambrechts, Laurens and Bonine, Noah and Verstraeten, Rita and Pardons, Marion and Noppe, Ytse and Rutsaert, Sofie and Van Nieuwerburgh, Filip and Van Criekinge, Wim and Cole, Basiel and Vandekerckhove, Linos}},
language = {{eng}},
publisher = {{Cold Spring Harbor Laboratory}},
series = {{BioRXiv}},
title = {{HIV-PULSE : a long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization}},
url = {{http://doi.org/10.1101/2023.01.18.524396}},
year = {{2023}},
}
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