Abstract
Mpox diagnosis relies on lesion swabs, which are infeasible when lesions are absent or inaccessible, limiting case detection during outbreaks and surveillance in resource-limited settings. This cross-sectional paired diagnostic study evaluated saliva, anorectal swabs, and urine as alternatives to lesion swabs (the reference standard) at the Entebbe Isolation Unit during Uganda’s 2024–2025 clade 1b outbreak. Among 120 participants (52.5% female; median age 28), 76.7% were PCR-positive. Positivity was highest for lesion swabs (83.3%), followed by saliva (81.7%), anorectal swabs (78.3%), and urine (75.8%). Viral loads did not differ significantly across specimen types, and saliva met the predefined diagnostic equivalence criteria relative to lesion swabs. Urine showed significant directional discordance. No sex-based differences in detection were observed. Here, we show that saliva is a noninvasive alternative to lesion swabs for mpox PCR diagnosis; anorectal swabs offer high sensitivity in mucosal exposure contexts; and urine is suboptimal as a standalone specimen.
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We acknowledge the National Health Laboratory and Diagnostic Services staff, especially those at the Central Emergency Response & Surveillance Laboratory, the Entebbe Regional Referral Laboratory, and the participating healthcare facilities, for their support. Special thanks to the Entebbe Isolation Unit and hospital staff for their cooperation.
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No funding was received for this study.
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Nsawotebba, A., Nakintu, V., Kabazzi, J. et al. Saliva, urine, and anorectal swabs as viable alternatives to lesion swabs for molecular diagnosis of mpox. Nat Commun (2026). https://doi.org/10.1038/s41467-026-73489-z
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DOI: https://doi.org/10.1038/s41467-026-73489-z
