Aircraft wastewater surveillance correlates with passenger SARS-CoV-2 variants detected during mandatory border testing

Introduction Global air travel plays a central role in the rapid international spread of infectious diseases, including SARS-CoV-2. While individual passenger testing has been widely used to monitor viral importation, it is resource-intensive and may miss asymptomatic cases. Aircraft wastewater surveillance has emerged as a non-invasive, scalable alternative for monitoring pathogen circulation among travelers. In this study, we evaluated the ability of aircraft wastewater to reflect SARS-CoV-2 variant distributions among passengers under real-world conditions. Methods Wastewater samples and matched clinical data were collected from 86 international flights (42 from the UK and 44 from the USA) arriving in Israel during May 2022, when mandatory SARS-CoV-2 testing of passengers was still in place. Wastewater samples were processed using standardized concentration and RNA extraction protocols, followed by RT-qPCR detection and whole-genome sequencing. Variant frequencies in wastewater were compared to those obtained from passenger clinical samples using bioinformatic pipelines and statistical analyses, including correlation testing. Results SARS-CoV-2 RNA was detected in over 90% of aircraft wastewater samples, despite low infection prevalence among passengers (1.8%–3.4%). Sequencing revealed that dominant variants in wastewater (primarily Omicron BA.2, followed by BA.5 and BA.4) were consistent with those identified in passenger samples and with globally circulating lineages. Strong correlations were observed between wastewater-derived and clinical variant distributions ( r = 0.84 for UK flights and r = 0.86 for USA flights). Viral load was positively associated with genome coverage, although it did not correlate with passenger numbers or infection rates. Discussion Aircraft wastewater surveillance reliably captured SARS-CoV-2 variant profiles among international travelers, even at low infection prevalence. While limitations such as variability in passenger behavior and incomplete genome coverage exist, this approach provides a sensitive and complementary tool to traditional surveillance methods. Integration of aircraft wastewater monitoring with existing genomic surveillance systems could enhance early detection of emerging variants and strengthen global public health preparedness.