Traveler-based Genomic Surveillance: A Scalable Approach to Early Pathogen Detection and Global Biosecurity

BackgroundIn September 2021, the U.S. Centers for Disease Control and Prevention (CDC) implemented the Traveler-based Genomic Surveillance (TGS) program, a surveillance system that leverages genomic sequencing of samples from international air travelers and aviation wastewater for early detection of infectious threats. MethodsDuring September 2021-August 2024, nasal samples were collected anonymously from volunteer international travelers arriving at eight U.S. airports. During February 2023- August 2024, aviation wastewater samples were collected from arriving flights. Nasal samples were pooled and sent to a laboratory for RT-PCR testing. Genomic sequencing was conducted for SARS-CoV-2 and respiratory, gastrointestinal (wastewater), and other pathogens of public health importance. FindingsNasal samples from 694,798 travelers were grouped into 67,308 pools and tested; 13,990 (20.8%) were positive for SARS-CoV-2. Over 80% (400/495) of airplane and 96{middle dot}6% (422/437) triturator (a wastewater collection point from multiple airplanes) samples were positive for SARS-CoV-2. Sequence results were made publicly available a median of 11 days (IQR 10- 13 days) after sample collection. Predominant SARS-CoV-2 variants changed over time. Positive tests for influenza virus and respiratory syncytial virus were high in December/January, and gastrointestinal viruses were detected in wastewater during all months. Monitoring was scaled in response to reported outbreaks of COVID-19 and Mycoplasma pneumoniae in China and clade 1 monkeypox virus in central Africa. InterpretationTraveler nasal and aviation wastewater sampling can provide critical early detection of infectious pathogens before widespread U.S. community transmission. The TGS program provides a model for integrated traveler-based genomic surveillance. FundingCDC Research in ContextO_ST_ABSEvidence before this projectC_ST_ABSWe searched PubMed for relevant studies published during December 1, 2020-August 31, 2024, using the terms "traveler surveillance", "wastewater monitoring", "SARS-CoV-2 genomics", and "airport-based surveillance", without language restrictions. Previous reports have shown the feasibility of using travelers as sentinel populations for disease surveillance. Modeling studies have proposed integrating genomic data into international travel surveillance systems to enhance early pathogen detection, and evidence from Australia, Canada, and the UK suggests such programs could be scalable and effective. Early pandemic-era wastewater surveillance, particularly aviation wastewater, demonstrated that air travel hubs can be used to monitor pathogen importation. Prior efforts largely focused on SARS-CoV-2, with limited integration of multi-pathogen surveillance or side-by-side comparisons of nasal and wastewater surveillance modalities. A limited number of public health reviews have examined the broader implications of airport-based surveillance, including novel methods like airplane wastewater testing. However, empirical data on sustained, large-scale implementation of these models especially outside of regulatory or mandatory testing frameworks have been sparse. Added value of this projectThis is the first real-world implementation and scale-up of an anonymized, multi-pathogen traveler-based surveillance system across multiple U.S. international airports. We developed a scalable framework that integrated nasal swab testing, airplane and airport wastewater sampling, with genomic sequencing into a unified pathogen surveillance platform. Unlike prior efforts which primarily focused on SARS-CoV-2, this program captured respiratory and gastrointestinal viruses simultaneously and tracked genomic variation in near-real time. The program transitioned from a pilot to a multi-modality national surveillance system in under four years, engaging nearly 700,000 international travelers, and nearly 1000 aviation wastewater samples. Our findings demonstrate the feasibility of rapidly adapting this infrastructure for emerging threats and underscores the importance of sentinel surveillance in addressing global sequencing blind spots. Implications of all the available evidenceThe successful scale-up and real-time application of the TGS program illustrates that traveler-based surveillance can serve as a critical global early warning tool. Data generated from this program have filled gaps in global pathogen tracking, informed public health responses to outbreaks, and demonstrated that surveillance of international travelers can be achieved without mandatory testing. The scalability, speed, and adaptability of the program offer a viable model for global replication, especially as routine surveillance capacities decline. Our findings suggest that integration of multi-modal, voluntary traveler surveillance including sequencing and wastewater-based epidemiology should be considered a core component of pandemic preparedness and response frameworks worldwide.