SARS-CoV-2 Intra-Host Evolution in 58 COVID-19 Patients with Serial Swabs

58 cases of COVID-19 with two or more consecutive positive swabs were analyzed for viral mutation dynamics. Whole genome sequences were processed using Nextclade and the Stanford Coronavirus Antiviral & Resistance Database to track minority mutations. The data, authored by Carla della Ventura and last updated in April 2026, suggests a mechanism of fitness selection for SARS-CoV-2 mutations during acute infection.

Use Cases

• Modeling mutation acquisition and loss over time based on serial swab comparisons.
• Investigating associations between patient comorbidities, like cardiovascular disease, and mutation rates.
• Comparing viral negativization periods across different SARS-CoV-2 variants such as BQ.1 and BA.1.
• Analyzing patterns of mutation prevalence in specific viral genes like the S gene and ORF1a.

Strengths

• Longitudinal data from 58 patients with multiple timepoints (T1, T2, T3).
• Analysis includes 57 hospitalized subjects with detailed clinical outcomes, including a 20.7% mortality rate.
• Variant calling was performed using established tools like Nextclade and a Stanford database.

Limitations

• Row count is unknown, which may limit suitability assessment.
• Column-level documentation is absent; field semantics must be inferred after download.
• The dataset is small, at 274.2 KB, indicating limited scope.

Provenance

Source

Carla della Ventura via figshare.

Collection Method

Whole genome sequencing of clinical swabs from hospitalized COVID-19 patients.

Freshness

Last updated 2026-04-28 05:28:08; freshness should be verified.