SARS-CoV-2 Detection in International Travelers Through Wastewater-Based #Epidemiology at the Kigali International Airport: Genomic #Surveillance Study
Background: Traditional infectious disease #Surveillance systems face significant limitations, including delayed detection, underreporting of asymptomatic cases, and inequitable healthcare access. Wastewater-based #Epidemiology (WBE), enhanced with genomic analysis, offers a non-invasive and cost-effective alternative for early pathogen detection and variant characterization, particularly valuable for monitoring international disease transmission. Objective: To implement and evaluate a genomics-enhanced WBE #Surveillance system for detecting and characterizing SARS-CoV-2 #COVID19 #coronavirus variants among international travelers at Kigali International Airport, Rwanda, and to assess its potential as an early warning system for pandemic preparedness. Methods: Between May and December 2023, we collected wastewater samples from international flights arriving at Kigali International Airport under Rwanda's National One Health strategy. Molecular detection was done using polymerase chain reaction (PCR) assays, followed by whole-genome sequencing of positive samples. Bioinformatics analysis included quality assessment with Nanoplot v.1.41.6, genome mapping using minimap2 v.2.26, and lineage identification using the Freyja tool v.1.4.5. Spatial and temporal analyses were used to identify transmission patterns and variant origins. Results: Of 630 wastewater samples collected from flights originating from nine countries, 603 were successfully processed, with 21.0% (132/617) testing positive for SARS-CoV-2 #COVID19 #coronavirus. Whole-genome sequencing was conducted on 33 samples, yielding an average viral sequence depth of 1,250 reads with 92% genome coverage (range: 78-97%). Genomic analysis identified seven SARS-CoV-2 #COVID19 #coronavirus variants, including Omicron subvariants XBB.1.5, XBB.1.16.6, EG.5.1, GE.1, and FE.1.1.1. Notably, 70% (23/33) of sequenced samples could not be assigned to existing lineages, suggesting potential novel variants. Most samples came from Qatar (21.4%, n=135), United Arab Emirates (19.5%, n=123), and the United Kingdom (19.4%, n=122). Positive samples were detected from 11 countries, with variants frequently found in flights from the United Kingdom, France, Belgium, Kenya, Tanzania, and South Africa. Sample collection capacity increased from six in week 1 to 33 by week 27. SARS-CoV-2 #COVID19 #coronavirus positivity rates showed seasonal variation, with a marked decline in June-July 2023. Conclusions: Genomics-enhanced WBE demonstrated high sensitivity for early detection of SARS-CoV-2 #COVID19 #coronavirus variants among international travelers, including potential novel variants undetectable through traditional #Surveillance. Its non-invasive and cost-effective nature, combined with the ability to generate population-level #Epidemiological insights, makes it particularly suitable for resource-limited settings. This approach supports Rwanda's National One Health strategy and offers a scalable model for advancing global health security in Sub-Saharan Africa through innovative #Surveillance tools.