Surveillance study uncovers hidden viral pathogens in test-negative respiratory samples, highlighting metagenomic sequencing utility for outbreak detection.
Key Points
Identify undetected viral pathogens responsible for acute respiratory infections in test-negative clinical specimens using an untargeted metagenomic workflow.
Evaluated N=300 previously test-negative nasopharyngeal samples across diverse clinical cohorts in Peru.
Amplified viral genomic material via sequence-independent single-primer amplification (SISPA) and sequenced samples on the Illumina platform.
Depleted human reads and performed taxonomic profiling with Kraken2, applying custom filtration thresholds based on reads per million ratios (RPMr), SMNR, and MAPQ scores.
Detected hidden viral pathogens in 35.66% of previously test-negative respiratory specimens.
Characterized a viral profile dominated by Coronaviridae (67.2%, predominantly SARS-CoV-2), followed by Picornaviridae (13.6%) and Orthoherpesviridae (12.0%).
Identified less frequent viral families including Paramyxoviridae (5.6%), Anelloviridae (0.8%), and Adenoviridae (0.8%).