Chikungunya Virus Genomic Sequencing Data for 13 Clinical Samples

Kaiying Wang published this dataset on 2026-04-27. It contains results from a systematic evaluation of four next-generation sequencing configurations for Chikungunya virus genomic surveillance, using 13 clinical samples with varying viral loads. The data compares sequencing depth, genome coverage, and variant detection between second-generation and third-generation platforms with different amplicon schemes.

Use Cases

• Benchmarking sequencing platform performance for viral variant detection based on the described comparison of second-generation and third-generation methods.
• Analyzing intra-host viral diversity in low viral load samples based on the reported detection of low-frequency variants.
• Studying coverage biases in challenging genomic regions like the capsid domain based on the described platform-specific performance.
• Training models to predict variant detection sensitivity from viral load (Ct values) based on the reported correlation analysis.

Strengths

• Includes data from 13 clinical samples with Ct values ranging from 17.41 to 38.14.
• Compares four specific sequencing configurations, reporting metrics like mean sequencing depth (152,430x) and genome coverage (99.9%).
• Reports on the detection of a broad spectrum of variants, including 1,553 unique variants identified by third-generation sequencing with 200-bp amplicons.
• Provides Ct-stratified analysis showing variant detection performance in ultra-low viral load samples.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Data may reflect methodological bias inherent to the specific sequencing platforms and amplicon schemes evaluated.

Provenance

Source

figshare

Collection Method

Systematic evaluation of sequencing configurations using clinical samples.

Time Range

The dataset was published in 2026, but the temporal coverage of the clinical samples is not specified.

Freshness

Last updated 2026-04-27 12:22:47; freshness should be verified.

Geography

The geographic origin of the 13 clinical samples is not specified.