Airplane wastewater as a gateway for pathogen surveillance

Air travel plays a key role in the global spread of many diseases, including COVID-19. Surveillance of international travelers is useful for the detection of emerging viruses and variants of concern, especially in a context of global relaxations in testing policy. We aimed to assess the feasibility of using wastewater surveillance from airplanes as a method for monitoring SARS-CoV-2 variants and other pathogens entering Belgium.

From January to March 2023, in the wake of the COVID pandemic, 32 wastewater samples were collected at Brussels Airport from direct flights originating in Beijing, China. We applied various qPCR panels and sequencing methods, including hybrid-capture metagenomic sequencing (Twist Bioscience) targeting more than fifteen thousand strains of known human and animal viruses.

Nineteen out of 32 samples tested positive for SARS-CoV-2. Various other pathogens, including enterovirus/rhinovirus, adenovirus, norovirus, adenovirus 40/41, and multiple clinically relevant bacteria, were identified using respiratory and gastrointestinal qPCR panels. In 7 samples, SARS-CoV-2 variants could be determined, belonging to known lineages BA4/BA5, BA4.6/BF7, and XBB. Moreover, hybrid-capture approach allowed us to recover complete genomes of viruses from families Polyomaviridae, Papillomaviridae, Herpesviridae as well as Aichivirus A and Hepatitis B virus.

This pilot project demonstrates the feasibility of detecting SARS-CoV-2 and its variants in wastewater of commercial airplanes. This method offers a valuable means of obtaining information from regions with limited SARS-CoV-2 genomic surveillance data. Moreover, using a hybrid-capture approach, a broad range of viruses of concern can be detected. The implementation of this novel screening approach is promising for enhancing traveler-based surveillance.