Saliva, urine, and anorectal swabs as viable alternatives to lesion swabs for molecular diagnosis of mpox

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. Mpox diagnosis typically depends on lesion swabs, which are impractical in certain settings. Here, the authors demonstrate that saliva can serve as a noninvasive alternative, while anorectal swabs are highly sensitive in mucosal exposure contexts, enhancing diagnostic strategies during outbreaks.