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Metagenomic sequencing of composite airplane wastewater for surveillance of emerging viruses

Abstract Robust early warning of emerging viruses requires sampling populations that drive spread coupled with assays capable of detecting new viral variants or species. Untargeted viral metagenomic sequencing can, in principle, detect any virus, including completely novel ones. Composite airplane wastewater enables monitoring long-distance travelers from central collection points; however, the performance of untargeted viral metagenomic sequencing in this sample type remains unknown. In municipal wastewater, abundant sewer-associated microbes and ribosomal RNA depress viral relative abundance, limiting metagenomic sensitivity. We compared untargeted viral metagenomic sequencing of composite airplane wastewater with time-matched municipal wastewater from the Greater Boston area. Human viruses and other human-associated taxa had consistently higher relative abundance in airplane samples than municipal samples, while most sewer-associated taxa had …

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