Universal Target Capture of HIV Sequences From NGS Libraries

Area of Science:

• Virology
• Genomics
• Bioinformatics

Background:

• Global HIV surveillance requires tracking viral evolution.
• Next-generation sequencing (NGS) advances allow direct sequencing from patient samples.
• A universal, sensitive method for HIV sequencing is still needed.

Purpose of the Study:

• To develop a novel HIV enrichment strategy for near-complete genome sequencing.
• To enhance sensitivity and sequencing capacity for low viral load specimens.
• To improve the monitoring of HIV sequence diversity.

Main Methods:

• Developed a biotin-labeled probe set (HIV-xGen) tiling all HIV-1 and HIV-2 strains.
• Captured viral cDNA from patient plasma via hybridization to probes.
• Sequenced enriched cDNA using Illumina MiSeq and aligned reads with CLC Bio software.

Main Results:

• HIV-xGen probes selectively captured and amplified HIV sequences, enriching reads by over 1,000-fold.
• Increased overall genome coverage by an average of 40% and enabled characterization of 50 new HIV strains.
• Achieved full-length genome coverage with a viral load cutoff of approximately log 3.5 copies/ml.

Conclusions:

• HIV-xGen allows characterization of over 20 complete HIV genomes per run.
• The method is versatile, capturing all HIV strains and sensitive to low viral loads.
• HIV-xGen is a valuable tool for global HIV sequence diversity monitoring.