ABSTRACT
Background. International travel facilitates SARS-CoV-2 spread globally. Early detection of variants among arriving international travelers could provide viral information about introduction of variants with differing infectivity, virulence, and vaccine effectiveness, enabling adjustments to treatment and prevention strategies. We initiated a genomic surveillance program at 4 US airports to detect SARS-CoV-2 variants among arriving international travelers. Methods. Between November 29, 2021-April 24, 2022, we enrolled arriving air travelers (>=18 years) from flights originating in 16 countries on 5 continents. At four airports, participants self-collected nasal swab samples that were pooled with 5-25 other samples by country of flight. Participants were also given a take-home saliva collection kit;saliva was collected 3-5 days after arrival and mailed back to the laboratory. SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) was performed on all samples at the laboratory. Positives underwent whole genome sequencing. Demographic, clinical, and travel information was collected. Results. We enrolled 28,656 travelers;median age was 42 years (interquartile range 31-55), 48% were female, and 99.4% self-reported COVID-19 vaccination. Overall, 19%(504/2,666) of pooled and 7.5%(285/3804) of individual samples were positive for SARS-CoV-2. Highest pool positivity of 46% occurred during January 3-10, 2022 (Figure 1).Omicron variant accounted for 97%of sequences (Figure 2).We detected the earliest reporting of Omicron sub-lineages BA.2 and BA.3 (7 and 43 days earlier than reported elsewhere) in the United States and North America, respectively. During April 4-18, we detected an increasing trend of pool positivity among travelers on South African flights, detecting one of the first US-reported BA.4 sub-lineages consistent with early surge of cases in South Africa. Weekly pooled positivity for travelers on South African flights aligned with World Health Organization (WHO)-reported 7-day COVID-19 incidence rates over the same period (Figure 3). ] Conclusion. This genomic sequencing surveillance platform is a model for traveler-based SARS-CoV-2 genomic surveillance that can be used as an early warning system to detect future outbreaks and pandemics. (Figure Presented).