A Review of Gastrointestinal and Respiratory Pathogen Detection in Wastewater: Implications for Early Warning and Public Health Surveillance

In Africa, the load of diarrheal and respiratory diseases is amplified by limited surveillance capacity, diagnostic limitations, and socioeconomic inequalities. In rapidly urbanizing settings such as Kigali (Rwanda), integrating wastewater-based epidemiology (WBE) into existing surveillance systems gives a promising strategy for generating real-time epidemiological intelligence, identifying community-level hotspots, and addressing gaps in traditional reporting systems. Gastrointestinal and respiratory infections remain major causes of morbidity and mortality globally, mainly in low- and middle-income countries (LMICs), where traditional clinical surveillance systems frequently underreport true disease burden. This review synthesizes present evidence on the detection of gastrointestinal and respiratory pathogens in wastewater and evaluates the utility of WBE for early warning and public health action. A narrative review approach was used to identify peer-reviewed literature, global health reports, and surveillance studies focusing on wastewater detection of gastrointestinal and respiratory pathogens. Databases including PubMed, Scopus, and Google Scholar were searched for studies published between 2000–2024. The search yielded 1,247 records, of which 312 duplicates were removed. After title/abstract screening, 228 full texts were assessed for eligibility. Ultimately, 96 studies met the inclusion criteria and were included in the final review. Reasons for exclusion included: lack of pathogen data (n=58), industrial focus (n=27), or insufficient methodological detail (n=47). WBE provides a non-invasive, cost-effective approach for monitoring symptomatic and asymptomatic infections. Challenges involve variability in sampling, environmental factors affecting viral decay, and differences in laboratory workflows. WBE is a powerful complement to traditional infectious disease surveillance, suggesting early warning capabilities, population-level coverage, and real-time insights into pathogen circulation. Integrating WBE into surveillance programs especially in LMICs such as Rwanda can significantly strengthen epidemic preparedness, guide resource allocation, and improve outbreak response. Sustained investment in laboratory capacity, standardized protocols, and multisector collaboration is essential to fully leverage WBE for public health protection.