<i>Notes from the Field:</i> Aircraft Wastewater Surveillance for Early Detection of SARS-CoV-2 Variants — John F. Kennedy International Airport, New York City, August–September 2022

Abstract

As SARS-CoV-2 testing declines worldwide, surveillance of international travelers for SARS-CoV-2 enables detection of emerging variants and fills gaps in global genomic surveillance (1).Because SARS-CoV-2 can be detected in feces and urine of some infected persons (2), wastewater surveillance in airports and on aircraft has been proposed by the global public health community † as a low-cost mechanism to monitor SARS-CoV-2 variants entering the United States.Sampling wastewater directly from aircraft can be used to link SARS-CoV-2 lineage data with flight origin countries without active engagement of travelers (3).During August 1-September 9, 2022, the biotech company Ginkgo Bioworks, in collaboration with CDC, evaluated the feasibility of SARS-CoV-2 variant detection in aircraft wastewater from incoming international flights.Aircraft wastewater samples were collected from selected flights from the United Kingdom, Netherlands, and France arriving at John F. Kennedy International Airport in New York City.Wastewater (approximately 0.25 gal [1 L]) was collected from each plane during normal maintenance using a device that attaches to the lavatory service panel port and the lavatory service truck hose.After concentration with affinity-capture magnetic nanoparticles (4), wastewater samples were tested for SARS-CoV-2 by reverse transcription-polymerase chain reaction (RT-PCR).§ Samples with cycle thresholds <40 underwent whole genome sequencing using ARTIC (version 4.1; ARTIC Network) primers.¶ Multiple lineages within samples were identified using Freyja, a tool for deconvolution of complex samples.**Sequences meeting quality control criteria (e.g., >70% genome coverage) † † were assigned to sublineages using

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