Supplementary file 3_Diagnostic sensitivity and specificity of metagenomic sequencing and

A supplementary file presents Bayesian latent class model estimates for the diagnostic sensitivity and specificity of nanopore metagenomic sequencing and qPCR tests. The analysis is based on 760 nasal swabs collected from calves and yearlings in 19 western Canadian feedlots for six bovine respiratory disease-associated viruses. The dataset was authored by Emmanuel Donbraye and last updated in March 2026.

Use Cases

• Compare diagnostic test performance (qPCR vs. metagenomic sequencing) for specific viruses like BCoV and BRSV based on the reported sensitivity and specificity estimates.
• Benchmark nanopore metagenomic sequencing as an alternative diagnostic method for bovine respiratory disease based on the comparative results described.
• Inform statistical modeling of diagnostic test accuracy in the absence of a gold standard based on the application of Bayesian latent class models.
• Study the prevalence and co-detection patterns of multiple viruses and bacteria associated with bovine respiratory disease in a feedlot setting.

Strengths

• Provides quantitative sensitivity and specificity estimates with 95% credible intervals for five viruses.
• Compares two modern diagnostic methods (qPCR and nanopore metagenomic sequencing) on the same 760 samples.
• Uses Bayesian latent class modeling, a robust statistical approach for test evaluation without a perfect gold standard.

Limitations

• Row count and column-level documentation are absent; field semantics must be inferred after download.
• Data is limited to 19 feedlots in western Canada, which may limit generalizability.
• The primary data format is a 521.2 KB PDF, which may require extraction for computational analysis.

Provenance

Source

figshare, author Emmanuel Donbraye.

Collection Method

Nasal swabs collected from fall-placed calves and yearlings at feedlot arrival, analyzed via commercial qPCR and in-house nanopore metagenomic sequencing.

Time Range

Collection time not specified; analysis publication date is 2026.

Freshness

Last updated 2026-03-17 13:07:31; freshness should be verified.

Geography

Samples from 19 western Canadian feedlots.