Spatiotemporal dynamics and phylogeography of HCoV-NL63 and HCoV-OC43 in Thailand, 2024–2025
- 1Department of Pediatrics, Faculty of Medicine, Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand
- 2Division of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- 3FRS(T), The Royal Society of Thailand, Bangkok, Thailand
Abstract
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.
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BibTeX
@article{puenpa2026spatiotemporal,
title = {{Spatiotemporal dynamics and phylogeography of HCoV-NL63 and HCoV-OC43 in Thailand, 2024–2025}},
author = {Jiratchaya Puenpa and Ratchadawan Aeemjinda and Preeyaporn Vichaiwattana and Sumeth Korkong and Yong Poovorawan},
journal = {PLOS One},
year = {2026},
month = sep,
doi = {10.1371/journal.pone.0357483},
url = {https://doi.org/10.1371/journal.pone.0357483},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Spatiotemporal dynamics and phylogeography of HCoV-NL63 and HCoV-OC43 in Thailand, 2024–2025
AU - Jiratchaya Puenpa
AU - Ratchadawan Aeemjinda
AU - Preeyaporn Vichaiwattana
AU - Sumeth Korkong
AU - Yong Poovorawan
PY - 2026
DA - 2026/09/08
JO - PLOS One
DO - 10.1371/journal.pone.0357483
UR - https://doi.org/10.1371/journal.pone.0357483
AB - 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.
SN - 1932-6203
ER -