JMIR Publications

ABSTRACT

Background:

The COVID-19 pandemic exposed critical limitations in global disease surveillance systems, particularly in resource-limited settings. Wastewater-based epidemiology (WBE) emerged as a promising surveillance tool, but its implementation in low-income countries and international travel hubs has been insufficiently explored.

Objective:

This study investigated the effectiveness of a novel genomics-enhanced WBE system for monitoring SARS-CoV-2 variants among international travelers at Rwanda's main port of entry.

Methods:

This was a prospective surveillance study conducted at Kigali International Airport between May and December 2023, implementing a dual-track approach combining aircraft wastewater analysis and voluntary passenger sampling. Wastewater samples were concentrated using Nanotrap® microbiome A particles, followed by RNA extraction and SARS-CoV-2 detection using RT-PCR. Positive samples meeting quality criteria (CT values ≤37) were subjected to whole genome sequencing using Oxford Nanopore Technology.

Results:

Among 630 wastewater samples collected from international flights, 21% (132/630) tested positive for SARS-CoV-2. Whole genome sequencing of 33 samples revealed seven distinct Omicron subvariants, including XBB.1.5, XBB.1.16.6, EG.5.1, GE.1, and FE.1.1.1. Notably, 23 sequences (70%) could not be assigned to existing lineages, suggesting potential novel variants. Most positive samples were associated with flights originating from the United Kingdom, France, Belgium, Kenya, Tanzania, United Arab Emirates, Qatar, Tanzania, South Africa, and Uganda. Temporal analysis showed significant variation in positivity rates, with a notable reduction between June and July 2023.

Conclusions:

This study demonstrates the feasibility and effectiveness of implementing genomics-enhanced WBE surveillance in a low-income country setting. The high proportion of unassigned sequences suggests ongoing SARS-CoV-2 evolution and emphasizes the need for continued genomic surveillance. This approach provides a cost-effective, non-invasive method for detecting emerging variants early and could be adapted to monitor other infectious diseases, contributing to global health security and pandemic preparedness.