Journal Article Epublish
PubMed: 40678396 DOI: 10.1016/j.ijregi.2025.100678
Early detection of SARS-CoV-2 variants using genomic surveillance: insights from aircraft wastewater and nasal swabs at Kigali International Airport, Rwanda.
IJID Reg 16:100678
Authors: Misbah Gashegu, Raissa Muvunyi, Jean Pierre Musabyimana, Esperance Umumararungu, Laetitia Irankunda, Chantal Mutezemariya, Arlene Uwituze, Nelson Gahima, John Rwabuhihi, Jean Claude Mugisha, Ayman Ahmed, Noel Gahamanyi, Leon Mutesa, Cecilia A Prator, Elizabeth A Landis, Casandra W Philipson, Nicole Bohme Carnegie, Albert Tuyishime, Isabelle Mukagatare, Noella Bigirimana, Claude Mambo Muvunyi
Affiliations
- Rwanda Biomedical Centre, Kigali, Rwanda.
- Africa Center of Excellency for Sustainable Cooling and Cold Chain (ACES), Kigali, Rwanda.
- School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.
- Pan-Africa One Health Institute, Kigali, Rwanda.
- Ginkgo Bioworks, Boston, MA, USA.
Abstract
Objectives
The growing threat of emerging infectious diseases necessitates proactive genomic surveillance, particularly, in regions with limited resources and low levels of existing reporting. This study highlights the implementation of a comprehensive genomic surveillance program at the Kigali International Airport and explores the utility of a dual-sample strategy leveraging environmental aircraft wastewater and pooled nasal swab sample types for comprehensive detection and characterization of SARS-CoV-2 lineages being imported into Rwanda.
Methods
Using a combined pooled nasal swab and aircraft wastewater sampling approach resulted in complementary insights in terms of geographic coverage, positivity, and variant characterization.
Results
Mutational profiling in source pooled nasal swabs and aircraft wastewater sample data revealed dynamic shifts in mutation prevalence that corresponded with global patterns. Emerging variant JN.1 was detected early in nasal swab data, demonstrating the power of using genomic surveillance as an early warning system.
Conclusions
These results support the feasibility of pathogen surveillance in high-traffic settings and may help drive interest in expanding programs to include pathogens beyond SARS-CoV-2.
MeSH
Sars-Cov-2, Aircraft, Airports, Severe Acute Respiratory Syndrome-Related Coronavirus