SARS-CoV-2 Detection in International Travelers Through Wastewater-Based Epidemiology at the Kigali International Airport: Genomic Surveillance Study

<h4>Background</h4>Traditional infectious disease surveillance systems face significant limitations, including delayed detection, underreporting of asymptomatic cases, and inequitable health care access. Wastewater-based epidemiology (WBE), enhanced with genomic analysis, offers a noninvasive and cost-effective alternative for early pathogen detection and variant characterization, particularly valuable for monitoring international disease transmission.<h4>Objective</h4>This study aimed to implement and evaluate a genomics-enhanced WBE surveillance system for detecting and characterizing SARS-CoV-2 variants among international travelers at the Kigali International Airport, Rwanda, and to assess its potential as an early warning system for pandemic preparedness.<h4>Methods</h4>Between May and December 2023, we collected wastewater samples from international flights arriving at the Kigali International Airport under Rwanda's National One Health strategy. Molecular detection was performed using polymerase chain reaction (PCR) assays, followed by whole-genome sequencing of positive samples. Bioinformatics analysis included quality assessment with Nanoplot (version 1.41.6), genome mapping using minimap2 (version 2.26), and lineage identification using the Freyja tool (version 1.4.5). Spatial and temporal analyses were used to identify transmission patterns and variant origins.<h4>Results</h4>Of 630 wastewater samples collected from flights originating from 9 countries, 603 were successfully processed, with 21% (132/617) testing positive for SARS-CoV-2. Whole-genome sequencing was conducted on 33 samples, yielding an average viral sequence depth of 1250 reads with 92% genome coverage (range 78%-97%). Genomic analysis identified 7 SARS-CoV-2 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%, 135/1630), the United Arab Emirates (19.5%, 123/1630), and the United Kingdom (19.4%, 122/1630). 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 6 in week 1 to 33 by week 27. SARS-CoV-2 positivity rates showed seasonal variation, with a marked decline in June-July 2023.<h4>Conclusions</h4>Genomics-enhanced WBE demonstrated a high sensitivity for the early detection of SARS-CoV-2 variants among international travelers, including potential novel variants undetectable through traditional surveillance. Its noninvasive 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.