Environmental surveillance as a tool for measles detection: Correlation with clinical cases in Pakistan

Measles remain a major public health challenge in high-burden settings such as Pakistan, where recurrent outbreaks are driven by gaps in immunization coverage and delayed detection of transmission. This study evaluated the utility of wastewater-based environmental surveillance (ES) as a complementary tool for measles monitoring in Karachi. Wastewater samples (n = 1,759) were collected from 32 surveillance sites across three towns between October 2023 and October 2024 and analyzed using the TaqMan Array Card (TAC) platform. Environmental detection trends were compared with reported clinical measles cases, and agreement between TAC and real-time RT-PCR was assessed using a subset of 310 samples. A significant association between wastewater measles detection and clinical cases was observed in Gulshan-e-Iqbal (β = 15.95, p = 0.008), with weaker or non-significant associations in other sites. Cross-correlation analysis identified site-specific lead–lag relationships, with wastewater signals preceding clinical cases by up to 12 weeks. After lag adjustment, associations strengthened across all towns, indicating a temporal link between environmental detection and reported cases. TAC demonstrated high specificity (93.39%) but limited sensitivity (36.51%) compared with RT-PCR. Genotyping of positive samples identified measles virus genotype B3, consistent with globally circulating strains. Overall, wastewater surveillance captured community-level measles transmission dynamics and provided early signals of outbreaks. Integration of ES into routine surveillance systems could strengthen early detection and outbreak response, particularly in resource-limited, high-transmission settings.