Quantifying virus load and characterising virus diversity in wildlife samples

We generated two metagenomic datasets from faecal samples collected from wild rodents in Eastern Uganda, using both target-enrichment and shotgun sequencing approaches. To assess the utility of target-enrichment for quantifying virus load, known concentrations of DNA and RNA viruses were spiked into faecal samples prior to sequencing. While shotgun sequencing was primarily used to characterise the diversity of viruses circulating in wild rodents, a subset of background samples was sequenced using both methods. This allowed a direct comparison of virus detection and recovery between the two approaches and provided insight into how sequencing strategy influences metagenomic outputs.