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Updated: Oct 3, 2025

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

Reconstructing viral haplotypes using long reads.

Dehan Cai¹, Yanni Sun¹

¹Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China.

Bioinformatics (Oxford, England)

|February 14, 2022

Summary

This summary is machine-generated.

RNA viruses rapidly evolve diverse genetic variants called haplotypes. A new tool, RVHaplo, reconstructs these viral haplotypes from long sequencing reads, improving upon existing methods for viral evolution studies.

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Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Published on: January 30, 2019

Area of Science:

Virology
Genomics
Bioinformatics

Background:

RNA viruses exhibit high mutation rates and lack proofreading, leading to diverse haplotype populations.
Characterizing viral haplotypes is crucial for understanding viral evolution and adaptation.
Short-read sequencing technologies have limitations in reconstructing complete viral haplotypes due to read length constraints.

Purpose of the Study:

To develop a novel computational tool, RVHaplo, for reconstructing viral haplotypes from long sequencing reads.
To evaluate RVHaplo's performance against existing tools using simulated and real viral sequencing data.
To enable accurate reconstruction of both common and rare viral haplotypes.

Main Methods:

Development of the RVHaplo algorithm for viral haplotype reconstruction.
Rigorous testing on simulated viral sequencing datasets.
Comparative analysis with established haplotype reconstruction tools using real viral sequencing data.

Main Results:

RVHaplo demonstrates superior performance in viral haplotype reconstruction from long reads compared to state-of-the-art methods.
The tool accurately identifies rare haplotypes (as low as 1% abundance) often missed by other approaches.
RVHaplo successfully reconstructs full-length or near-full-length viral haplotypes.

Conclusions:

RVHaplo offers a significant advancement in viral haplotype reconstruction, particularly from long-read sequencing data.
The tool enhances the ability to study viral population dynamics and evolution.
RVHaplo provides a valuable resource for researchers in virology and infectious disease.