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Unbiased Deep Sequencing of RNA Viruses from Clinical Samples
Published on: July 2, 2016
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MrHAMER2: high-accuracy long-read RNA sequencing to decode isoform-specific variation in viral transcripts during
Christian M Gallardo1, Jessica L Albert1, Andrew A Qazi2
1Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA.
Biorxiv : the Preprint Server for Biology
|July 14, 2025
Summary
Alternative splicing (AS) in HIV-1 infection is poorly understood during latency. A new sequencing method, MrHAMER2, accurately decodes viral RNA, revealing significant changes in HIV-1 isoforms with intron retentions during latency.
Area of Science:
- Molecular Biology
- Virology
- Genomics
Background:
- Alternative splicing (AS) expands protein diversity and is exploited by viruses like HIV-1.
- Understanding HIV-1 gene expression during latency is crucial but challenging due to low transcript abundance.
Purpose of the Study:
- To characterize the spliced HIV-1 transcriptome during latency.
- To evaluate the utility of the MrHAMER2 sequencing method for studying viral isoforms.
Main Methods:
- Utilized MrHAMER2, a high-accuracy long-read RNA sequencing method with dual Unique Molecular Identifier (UMI) tagging.
- Applied MrHAMER2 to a primary CD4+ T cell model of HIV-1 latency.
Main Results:
- Accurately captured and quantified full-length HIV-1 isoforms with high dynamic range and single-nucleotide accuracy.
- Identified substantial changes in viral isoforms, including increased intron retentions, during latency.
Conclusions:
- MrHAMER2 effectively decodes the complex spliced HIV-1 transcriptome in latency.
- Changes in HIV-1 isoforms during latency impact their translatable protein potential.
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