Detectability of Pathogenic RNA Virus Families in Different Body Sites: A Scoping Review

Nucleic acid amplification tests (NAATs) are central to modern virology diagnostics. However, evidence supporting alternative specimen types remains uneven across viral families, especially for emerging viruses. This limits diagnostic flexibility in outbreak and clinically complex settings. We conducted a scoping review of NAAT detectability across key body sites for human RNA viruses. PubMed and Embase were systematically searched for studies reporting NAAT results from urine, blood, fecal, cerebrospinal fluid, or respiratory specimens. Data were independently screened and synthesized to summarize specimen-specific detectability for each virus. From 8676 screened records, 321 studies were included, covering 39 viruses across 25 RNA virus families. Detectability across specimen types varied substantially between viruses. Consistent detection across multiple specimens was observed for few viruses, including SARS-CoV-2, Zika virus, and HIV, whereas many emerging viruses were evaluated in a single body compartment with limited comparative data. NAAT performance across specimen types is highly virus-specific and unevenly studied, with reliance on blood or respiratory specimens, potentially overlooking viable, less invasive alternatives. Evidence gaps are particularly pronounced for urine and cerebrospinal fluid, and heterogeneous reporting limits cross-study comparability. Standardized, cross-specimen and longitudinal studies are needed to improve diagnostic strategies, outbreak preparedness, and future assay development.