Genomic Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 Variants in Airport and Port Wastewaters, Republic of Korea, 2025.

ObjectivesThis study aims to examine the mutation status of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater samples collected from airports and ports, monitor variant trends, and provide baseline data for the early detection of emerging variants.MethodsWastewater samples were collected from 13 quarantine stations and tested for pathogens using TaqMan Array Card polymerase chain reaction. Whole-genome sequencing was conducted on SARS-CoV-2-positive samples, and the relative proportions of all SARS-CoV-2 lineages present in the wastewater samples were calculated using the Freyja analytical method.ResultsAnalysis of 382 specimens subjected to whole-genome sequencing demonstrated that NB.1.8.1 increased in airport and port wastewater samples after March, reaching a peak prevalence of 64.0% in August. Thereafter, the sublineage PQ.2 increased to 38.9% in November. Conversely, aircraft and ship wastewater samples were predominantly characterized by XFG rather than NB.1.8.1 and PQ.2, in line with global variant circulation trends.ConclusionsWastewater surveillance at airports and ports is anticipated to play a complementary role in existing clinical monitoring by allowing the early detection of imported cases and offering continuous monitoring of community transmission.