Spatiotemporal dynamics and phylogeography of HCoV-NL63 and HCoV-OC43 in Thailand, 2024–2025

Endemic human coronaviruses (HCoVs) HCoV-NL63 and HCoV-OC43 are common causes of acute respiratory infections (ARI), yet integrated surveillance and genomic data from Southeast Asia remain limited. We characterized HCoV-NL63 and HCoV-OC43 circulation in Thailand, during 2024-2025 using routine real-time RT-PCR testing, partial spike sequencing, and time-scaled phylogenetic analyses with global references. Among 11,709 ARI specimens, 329/8,122 were HCoV-positive in 2024 (4.05%) and 131/3,587 in 2025 (3.65%). Positivity was strongly seasonal, peaking in winter, and SARS-CoV-2 surges in the same testing stream generally coincided with lower endemic HCoV positivity. Genotype composition differed by virus: HCoV-OC43 was dominated by genotypes K and J at near-equal frequencies (48.3% and 47.2%), whereas HCoV-NL63 was mainly genotype C4 (43.6%), followed by B2 (32.7%) and C3 (20.9%). Time-scaled phylogenies placed Thai sequences across multiple regions of global diversity, consistent with repeated introductions and onward transmission within several co-circulating lineages. Estimated substitution rates were 3.86 × 10-4 substitutions/site/year for HCoV-NL63 and 9.27 × 10-4 for HCoV-OC43. Discrete-trait phylogeography supported bidirectional connectivity involving Thailand, with virus-specific differences in the most supported routes. Skygrid reconstructions suggested declines in genetic diversity after 2020, overlapping the COVID-19 era, with a more pronounced decrease for HCoV-OC43. Evidence for selection was limited and inconsistent for HCoV-NL63, whereas several HCoV-OC43 sites overlapped codon-based signals of diversifying selection. Overall, these findings provide a baseline for endemic HCoV seasonality, genotype composition, and connectivity in Thailand, and support continued genomic surveillance in Southeast Asia.