{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Pediatrics, Faculty of Medicine, Center of Excellence in Clinical Virology, Chulalongkorn University, Bangkok, Thailand",
    "Division of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand",
    "FRS(T), The Royal Society of Thailand, Bangkok, Thailand"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Jiratchaya Puenpa"
    },
    {
      "affs": [
        1
      ],
      "name": "Ratchadawan Aeemjinda"
    },
    {
      "affs": [
        2
      ],
      "name": "Preeyaporn Vichaiwattana"
    },
    {
      "name": "Sumeth Korkong"
    },
    {
      "name": "Yong Poovorawan"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/7kka3atbnrd70.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pone.0357483",
  "fulltext_url": null,
  "id": "7kka3atbnrd70",
  "issns": [
    "1932-6203"
  ],
  "landing_url": "https://doi.org/10.1371/journal.pone.0357483",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "2713|Respiratory viral infections research"
    ],
    [
      "plos",
      "/Biology and life sciences/Biogeography/Phylogeography"
    ],
    [
      "plos",
      "/Biology and life sciences/Evolutionary biology/Evolutionary systematics/Phylogenetics"
    ],
    [
      "plos",
      "/Biology and life sciences/Evolutionary biology/Evolutionary systematics/Phylogenetics/Phylogenetic analysis"
    ],
    [
      "plos",
      "/Biology and life sciences/Evolutionary biology/Population genetics/Phylogeography"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Population genetics/Phylogeography"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Viral pathogens/Coronaviruses"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Viral pathogens/Coronaviruses/SARS coronavirus/SARS CoV 2"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Viruses/RNA viruses/Coronaviruses"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Viruses/RNA viruses/Coronaviruses/SARS coronavirus/SARS CoV 2"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Viruses/Viral pathogens/Coronaviruses"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Viruses/Viral pathogens/Coronaviruses/SARS coronavirus/SARS CoV 2"
    ],
    [
      "plos",
      "/Biology and life sciences/Population biology/Population genetics/Phylogeography"
    ],
    [
      "plos",
      "/Biology and life sciences/Taxonomy/Evolutionary systematics/Phylogenetics"
    ],
    [
      "plos",
      "/Biology and life sciences/Taxonomy/Evolutionary systematics/Phylogenetics/Phylogenetic analysis"
    ],
    [
      "plos",
      "/Computer and information sciences/Data management/Taxonomy/Evolutionary systematics/Phylogenetics"
    ],
    [
      "plos",
      "/Computer and information sciences/Data management/Taxonomy/Evolutionary systematics/Phylogenetics/Phylogenetic analysis"
    ],
    [
      "plos",
      "/Earth sciences/Geography/Biogeography/Phylogeography"
    ],
    [
      "plos",
      "/Ecology and environmental sciences/Biogeography/Phylogeography"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Viral pathogens/Coronaviruses"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Viral pathogens/Coronaviruses/SARS coronavirus/SARS CoV 2"
    ],
    [
      "plos",
      "/People and places/Geographical locations/Asia/Thailand"
    ],
    [
      "plos",
      "/People and places/Geographical locations/Europe"
    ],
    [
      "plos",
      "/People and places/Population groupings/Ethnicities/Asian people/Thai people"
    ]
  ],
  "openalex": "W7211971024",
  "pdf_url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0357483&type=printable",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-08",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/7kka3atbnrd70.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:56Z",
      "native_id": "10.1371/journal.pone.0357483",
      "source": "plos",
      "url": "https://doi.org/10.1371/journal.pone.0357483"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "plos:evolutionary biology",
      "subfield": "evolutionary-biology"
    },
    {
      "field": "biology",
      "origin": "plos:microbiology",
      "subfield": "microbiology"
    }
  ],
  "title": "Spatiotemporal dynamics and phylogeography of HCoV-NL63 and HCoV-OC43 in Thailand, 2024–2025",
  "title_text": "Spatiotemporal dynamics and phylogeography of HCoV-NL63 and HCoV-OC43 in Thailand, 2024–2025",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:56Z",
  "url": "https://research.draconitic.com/paper/7kka3atbnrd70",
  "venue": "PLOS One",
  "versions": []
}