Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing

Area of Science:

• Virology
• Genomics
• Bioinformatics

Background:

• High-throughput sequencing (HTS) generates extensive data for herpes simplex virus (HSV) strains, crucial for understanding viral pathogenicity.
• Assembling complete herpesviral genomes is challenging due to repetitive regions and genetic variation in isolates.
• Existing HTS sequence assembly pipelines face difficulties with these complexities.

Purpose of the Study:

• To evaluate two approaches for identifying genetic variants in HSV1 strains using Illumina short-read sequencing data.
• To compare the efficacy of reference-based versus de novo assembly for variant identification in HSV1.
• To assess the impact of non-redundant reference genomes on variant discovery.

Main Methods:

• Two primary methods were evaluated: reference-based variant identification and de novo assembly-based variant identification.
• Both approaches utilized Illumina short-read sequencing data from HSV1 strains.
• A non-redundant reference genome was constructed to minimize low-complexity regions.

Main Results:

• Approximately 85% of genetic variants were identified irrespective of the chosen approach.
• The reference-based approach identified an additional 15% of variants, potentially due to viral passage and divergence from the reference.
• Reference-based approaches were less labor-intensive and identified variants across the entire genome, unlike de novo assembly, which is limited by successfully assembled contigs.

Conclusions:

• Reference-based approaches are recommended for variant discovery in viruses with well-assembled reference genomes, such as HSV1.
• De novo assembly can be prone to false variant identification in poorly assembled regions.
• Reference-based methods offer a more comprehensive and efficient strategy for HSV1 genetic variant analysis.