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NanoHIVSeq: A Long-Read Bioinformatics Pipeline for High-Throughput Processing of HIV Env Sequences
Zizhang Sheng1, Qin Xiao1, Yujie Qiao1
1Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
Biorxiv : the Preprint Server for Biology
|February 27, 2026
Summary
NanoHIVSeq simplifies HIV-1 envelope gene sequencing using Oxford Nanopore Technology. This UMI-free pipeline accurately recovers full-length viral variants, enabling efficient large-scale studies.
Area of Science:
- Genomics
- Virology
- Bioinformatics
Background:
- HIV-1 envelope (Env) gene sequencing is crucial for epidemiology and therapeutic development.
- Traditional methods like single-genome amplification (SGA) are low-throughput and labor-intensive.
- Oxford Nanopore Technology (ONT) offers long-read sequencing but faces challenges with high error rates.
Purpose of the Study:
- To develop a UMI-free, reference-free bioinformatics pipeline for accurate HIV-1 Env sequencing using ONT data.
- To enable efficient recovery of full-length functional Env variants from bulk PCR amplicons.
Main Methods:
- Introduction of NanoHIVSeq, a UMI-free bioinformatics pipeline for ONT data.
- Multistep clustering, consensus polishing, indel correction, denoising, and genotyping.
- Utilized ONT duplex sequencing technology with plasmid and HIV reservoir datasets.
Main Results:
- NanoHIVSeq demonstrated high robustness, recovery rate, reproducibility, and accuracy (>99.9% or >Q30).
- Performance was comparable to UMI-based approaches.
- Successful recovery of functional full-length Env variants.
Conclusions:
- NanoHIVSeq provides a flexible and simplified approach for ONT library preparation.
- Enables reproducible and efficient HIV-1 Env sequencing, particularly for large cohorts.
- Facilitates epidemiological studies, virus-antibody coevolution research, and therapeutic evaluations.
