A Pilot Surveillance Program to Identify Emerging SARS-CoV-2 Variants in International Travelers Arriving at a Major International Airport: Prospective Cohort Evaluation

Background: Testing arriving international travelers for COVID-19 paired with whole-genome sequencing (WGS) may identify new introductions of SARS-CoV-2 variants of concern in California, enabling a timely public health response. Traveler genomic surveillance may be a way to improve gaps in worldwide disease genomic surveillance. Objective: This paper aimed to describe a pilot surveillance program to identify SARS-CoV-2 variants in arriving international travelers at San Francisco International Airport (SFO). Methods: The California Department of Public Health implemented a pilot program at SFO to voluntarily test arriving international travelers for COVID-19 from June 2021 to November 2021 to identify SARS-CoV-2 variants. Arriving international travelers were offered self-collect COVID-19 antigen tests upon arrival at SFO. Travelers with positive COVID-19 antigen tests or with COVID-19 symptoms were recommended to self-collect and mail an additional specimen for diagnostic molecular testing. WGS of SARS-CoV-2 was performed on RNA extracts from positive tests to identify variants. Results: In total, 2.1% (19,008/892,558) of all arriving international travelers at SFO from 133 different countries of departure enrolled in the program. The COVID-19 test positivity among this group was 0.7% (33/5038), and the weekly test positivity range, 0% to 1.5%, was lower than the weekly test positivity across the state of California during the same time frame. Arriving international travelers departing from Turkey (3/145, 2.1%), Mexico (7/602, 1.2%), and the United Kingdom (6/626, 1.0%) had the highest test positivity. Of the 14 positive molecular tests, 10 (71.4%) were sequenced, and all were found to belong to the SARS-CoV-2 Delta B.1.617.2 lineage, the most prevalent SARS-CoV-2 variant in California and worldwide at the time. Conclusions: Voluntary testing of arriving international travelers paired with WGS was operationally and logistically feasible. Although the number of sequenced positive COVID-19 specimens in this program was limited, the lessons learned from this pilot informed improvements to subsequent iterations of traveler viral genomic surveillance in California and highlighted the potential value of traveler viral genomic surveillance to support early identification and characterization of emerging infectious diseases entering a region.