Molecular diagnostics reveal substantial sub-patent schistosomiasis and soil-transmitted helminth infections in school children: an implication for elimination programme

• Molecular diagnostics detected 44.6% more infections than microscopy (n=7,560) • Microscopy sensitivity estimated at only 69% by Bayesian latent class analysis • One-third of helminth infections remain undetected across six Nigerian states • Open defecation doubled infection odds (AOR: 2.1; 95% CI: 1.4–3.2) • WHO elimination thresholds may need recalibration for sub-patent infections Schistosomiasis and soil-transmitted helminthiasis elimination programmes rely on microscopic diagnostics, yet molecular methods may detect sub-patent infections invisible to conventional screening. To quantify sub-patent parasitic infections undetected by microscopy and estimate true prevalence using latent class analysis among primary school children across six Nigerian states. We conducted a multi-state cross-sectional study among 7,560 systematically sampled primary school children from Plateau, Rivers, Ebonyi, Kano, Benue, and Ondo States. All participants provided urine and stool specimens analysed using standard microscopy. A stratified random subset of 3,236 samples (42.8%) underwent molecular confirmation using multiplex PCR and quantitative real-time PCR. Bayesian latent class analysis estimated true prevalence accounting for imperfect sensitivity of both diagnostic methods. Microscopy revealed overall parasitic infection prevalence of 20.7% (1,565/7,560; 95% CI: 19.8–21.7%). Among the molecular subset (n=3,236), PCR detected 983 positive cases versus 680 by microscopy (44.6% increase; 95% CI: 40.8–48.5%; p<0.001). Latent class analysis estimated true prevalence at 24.8% for soil-transmitted helminths (95% CI: 23.5–26.2%) and 10.2% for schistosomiasis (95% CrI: 9.4–11.1%), indicating microscopy sensitivity of 69.1% (95% CrI: 66.4–71.7%) and molecular sensitivity of 94.1% (95% CI: 92.5–95.5%). Open defecation was independently associated with infection (adjusted odds ratio: 2.1; 95% CI: 1.4–3.2; p=0.001). Significant geographic variation was observed, with prevalence highest in Rivers State (24.2%) and lowest in Kano State (16.4%). Approximately one-third of parasitic infections remain undetected by microscopy across diverse Nigerian ecological zones. Integration of molecular diagnostics into elimination programmes both during active control to identify and treat sub-patent reservoir infections and during post-elimination surveillance to verify interruption of transmission is essential for accurate progress assessment towards the 2030 targets. WHO elimination thresholds may require recalibration to account for systematic underestimation by conventional diagnostics.