Abstract
SARS-CoV-2 continues to cause recurrent waves in the post-pandemic period, yet genomic data from Southeast Asia remain limited for several emerging Omicron lineages, including NB.1.8.1. In this study, routine acute respiratory infection (ARI) surveillance performed in Bangkok, Thailand, from January to December 2025 was integrated with real-time RT-PCR testing and complete spike-gene sequencing for lineage assignment and evolutionary analysis. Among 4756 ARI specimens, 473 (9.9%) tested positive for SARS-CoV-2. Positivity increased in late April, peaked in May (epidemiological week 21; 58.4%), and declined through late June. Lineage typing was successful for 165/473 positive samples (34.9%), identifying 16 Pango lineages. Early 2025 showed heterogeneous circulation, including XEC- and XEC.8-related lineages, whereas NB.1.8.1 predominated during the main wave, accounting for 92.4% of typed cases in May and 89.8% in June. No recombination signals meeting predefined criteria were detected in the spike dataset. The mean spike substitution rate was estimated at 1.11 × 10(-3) substitutions/site/year (95% HPD, 9.13 × 10(-4)-1.31 × 10(-3)), and the major Thai-containing NB.1.8.1 clade had an estimated tMRCA of 17 July 2024. These findings show that routine ARI surveillance combined with spike-based genomics can provide timely insights into SARS-CoV-2 circulation, lineage replacement, and ongoing viral evolution in Thailand.