Seasonal Coronavirus Infection

Infectious Disease Pathograph 2 Show in embeddings browser Viral Respiratory Infection

Seasonal (endemic) coronavirus infection is an acute respiratory infection caused by the four endemic human coronaviruses — HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1. These viruses circulate globally in a seasonal (winter-dominant) epidemic pattern and account for a substantial proportion of common cold cases across all age groups. They typically cause mild-to-moderate upper respiratory infection but can cause lower respiratory infection, otitis media, asthma exacerbations, and complications in infants, the elderly, and immunocompromised hosts. The four viruses differ in their host-cell receptor usage (e.g., HCoV-NL63 uses ACE2, the SARS-CoV-2 receptor; HCoV-229E uses aminopeptidase N; HCoV-OC43/HKU1 use 9-O-acetylated sialic acid).

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2
Pathophys.
5
Phenotypes
2
Pathograph
1
Medical Actions
1
Datasets
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Pathophysiology

2
Upper Respiratory Epithelial Infection
The endemic human coronaviruses infect the respiratory epithelium, where viral replication elicits an innate antiviral/interferon and inflammatory response. They typically produce mild-to-moderate upper respiratory illness resembling the common cold. The four viruses use different host-cell receptors, reflecting distinct tropism within the shared respiratory niche.
respiratory epithelial cell CL:0002632 Cell Ontology (CL) Relation: this pathophysiological event involves this cell type This pathophysiological event involves respiratory epithelial cell, annotated with epithelial cell of lower respiratory tract (CL:0002632). CL:0002632 is a cell type from the Cell Ontology. ciliated airway epithelial cell CL:0000064 Cell Ontology (CL) Relation: this pathophysiological event involves this cell type This pathophysiological event involves ciliated airway epithelial cell, annotated with ciliated cell (CL:0000064). CL:0000064 is a cell type from the Cell Ontology.
viral genome replication GO:0019079 Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves viral genome replication (GO:0019079). GO:0019079 is a biological process from the Gene Ontology. defense response to virus GO:0051607 Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves defense response to virus (GO:0051607). GO:0051607 is a biological process from the Gene Ontology. inflammatory response GO:0006954 Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves increased inflammatory response (GO:0006954). GO:0006954 is a biological process from the Gene Ontology. ↑ INCREASED
respiratory system UBERON:0001004 Uberon multi-species anatomy ontology (UBERON) Relation: this pathophysiological event occurs in this anatomical location This pathophysiological event occurs in respiratory system (UBERON:0001004). UBERON:0001004 is an anatomical location from the Uberon multi-species anatomy ontology.
Downstream
Lower Respiratory and Complicated Infection In vulnerable hosts, endemic coronavirus infection can extend beyond the upper airway to cause lower respiratory and complicated disease.
Show evidence (2 references)
PMID:33186086 SUPPORT Other
"Coronaviruses OC43, 229E, NL63, and HKU1 are endemic human respiratory coronaviruses that typically cause mild to moderate upper respiratory infections, similar to the common cold."
Identifies the four endemic human coronaviruses and establishes mild-to-moderate upper respiratory infection (common cold) as the typical presentation. Evidence source is OTHER as this is a review article.
PMID:41295541 SUPPORT Other
"Seasonal human coronaviruses (HCoVs), including HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1, circulate globally in an epidemic pattern and account for a substantial proportion of common cold cases, particularly in infants, the elderly, and immunocompromised individuals."
Establishes the seasonal/epidemic circulation of the four endemic HCoVs and their substantial contribution to common cold burden. Evidence source is OTHER as this is a review article.
Lower Respiratory and Complicated Infection
Although usually mild, the endemic human coronaviruses can cause lower respiratory infection, otitis media, asthma exacerbations, gastroenteritis, and occasional systemic complications, particularly in infants, the elderly, and patients with comorbidities.
inflammatory response GO:0006954 Gene Ontology (GO) Relation: this pathophysiological event involves this biological process This pathophysiological event involves increased inflammatory response (GO:0006954). GO:0006954 is a biological process from the Gene Ontology. ↑ INCREASED
lung UBERON:0002048 Uberon multi-species anatomy ontology (UBERON) Relation: this pathophysiological event occurs in this anatomical location This pathophysiological event occurs in lung (UBERON:0002048). UBERON:0002048 is an anatomical location from the Uberon multi-species anatomy ontology.
Show evidence (1 reference)
PMID:33186086 SUPPORT Other
"They also may cause simple and complicated lower respiratory infections, otitis media, asthma exacerbations, gastroenteritis, and a few systemic complications."
Documents the broader and complicated manifestations beyond the common cold. Evidence source is OTHER as this is a review article.
⬡

Pathograph

Use the checkboxes to hide or show graph categories. Hover nodes for evidence and cross-linked metadata.
Pathograph: causal mechanism network for Seasonal Coronavirus Infection Interactive directed graph showing how pathophysiology mechanisms, phenotypes, genetic factors and variants, experimental models, environmental triggers, and treatments relate through causal and linked edges.
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Phenotypes

5
Head and Neck 1
Nasal Congestion HP:0001742 Human Phenotype Ontology (HP) Relation: this clinical feature is this phenotype This clinical feature is Nasal congestion (HP:0001742). HP:0001742 is a phenotype from the Human Phenotype Ontology.
Immune 1
Pneumonia HP:0002090 Human Phenotype Ontology (HP) Relation: this clinical feature is this phenotype This clinical feature is Pneumonia (HP:0002090). HP:0002090 is a phenotype from the Human Phenotype Ontology.
Show evidence (1 reference)
PMID:33186086 SUPPORT Other
"They also may cause simple and complicated lower respiratory infections, otitis media, asthma exacerbations, gastroenteritis, and a few systemic complications."
Supports lower respiratory tract infection as a possible manifestation. Evidence source is OTHER as this is a review article.
Metabolism 1
Fever HP:0001945 Human Phenotype Ontology (HP) Relation: this clinical feature is this phenotype This clinical feature is Fever (HP:0001945). HP:0001945 is a phenotype from the Human Phenotype Ontology.
Respiratory 2
Rhinorrhea HP:0031417 Human Phenotype Ontology (HP) Relation: this clinical feature is this phenotype This clinical feature is Rhinorrhea (HP:0031417). HP:0031417 is a phenotype from the Human Phenotype Ontology.
Cough HP:0012735 Human Phenotype Ontology (HP) Relation: this clinical feature is this phenotype This clinical feature is Cough (HP:0012735). HP:0012735 is a phenotype from the Human Phenotype Ontology.
💊

Medical Actions

1
Supportive Care
Action: Supportive CareNCI Thesaurus (NCIT) Relation: this treatment is this clinical intervention This treatment is Supportive Care (NCIT:C15747). NCIT:C15747 is a clinical intervention from the NCI Thesaurus. NCIT:C15747
Management of endemic seasonal coronavirus infection is supportive; no specific antiviral therapy or licensed vaccine is currently available.
📊

Related Datasets

1
Molecular landscape of respiratory infection: A large-scale, multi-centre blood transcriptome dataset geo:GSE282464
Respiratory infections pose significant challenges to global health, impacting millions of individuals annually. Understanding the molecular mechanisms underlying the pathogenicity of these infections is crucial for developing effective interventions. RNA sequencing provides insights into a patient’s global transcriptome changes, facilitating the identification of host gene signatures in response to infection and potential therapeutic targets.
human BULK RNA SEQ n=377
PMID:40640204
Identified by GEO DataSets index search for Seasonal Coronavirus Infection (scripts/discover_datasets.py); accession and metadata verified against NCBI E-utilities on 2026-08-01. Title, sample count, and organism are GEO's own values.
{ }

Source YAML

click to show 
name: Seasonal Coronavirus Infection
creation_date: "2026-06-28T00:00:00Z"
description: >
  Seasonal (endemic) coronavirus infection is an acute respiratory infection
  caused by the four endemic human coronaviruses — HCoV-229E, HCoV-NL63,
  HCoV-OC43, and HCoV-HKU1. These viruses circulate globally in a seasonal
  (winter-dominant) epidemic pattern and account for a substantial proportion of
  common cold cases across all age groups. They typically cause mild-to-moderate
  upper respiratory infection but can cause lower respiratory infection, otitis
  media, asthma exacerbations, and complications in infants, the elderly, and
  immunocompromised hosts. The four viruses differ in their host-cell receptor
  usage (e.g., HCoV-NL63 uses ACE2, the SARS-CoV-2 receptor; HCoV-229E uses
  aminopeptidase N; HCoV-OC43/HKU1 use 9-O-acetylated sialic acid).
category: Infectious Disease
parents:
- Viral Respiratory Infection
synonyms:
- Endemic human coronavirus infection
- Common cold coronavirus
- HCoV-229E/NL63/OC43/HKU1 infection
pathophysiology:
- name: Upper Respiratory Epithelial Infection
  conforms_to: "innate_antiviral_interferon_response#Interferon-Stimulated Gene Antiviral State"
  description: >
    The endemic human coronaviruses infect the respiratory epithelium, where viral
    replication elicits an innate antiviral/interferon and inflammatory response.
    They typically produce mild-to-moderate upper respiratory illness resembling
    the common cold. The four viruses use different host-cell receptors, reflecting
    distinct tropism within the shared respiratory niche.
  cell_types:
  - preferred_term: respiratory epithelial cell
    term:
      id: CL:0002632
      label: epithelial cell of lower respiratory tract
  - preferred_term: ciliated airway epithelial cell
    term:
      id: CL:0000064
      label: ciliated cell
  biological_processes:
  - preferred_term: viral genome replication
    term:
      id: GO:0019079
      label: viral genome replication
  - preferred_term: defense response to virus
    term:
      id: GO:0051607
      label: defense response to virus
  - preferred_term: inflammatory response
    term:
      id: GO:0006954
      label: inflammatory response
    modifier: INCREASED
  locations:
  - preferred_term: respiratory system
    term:
      id: UBERON:0001004
      label: respiratory system
  evidence:
  - reference: PMID:33186086
    reference_title: "Complicating Infections Associated with Common Endemic Human Respiratory Coronaviruses."
    supports: SUPPORT
    evidence_source: OTHER
    snippet: >-
      Coronaviruses OC43, 229E, NL63, and HKU1 are endemic human respiratory
      coronaviruses that typically cause mild to moderate upper respiratory
      infections, similar to the common cold.
    explanation: >-
      Identifies the four endemic human coronaviruses and establishes
      mild-to-moderate upper respiratory infection (common cold) as the typical
      presentation. Evidence source is OTHER as this is a review article.
  - reference: PMID:41295541
    reference_title: "Current Status and Challenges of Vaccine Development for Seasonal Human Coronaviruses."
    supports: SUPPORT
    evidence_source: OTHER
    snippet: >-
      Seasonal human coronaviruses (HCoVs), including HCoV-229E, HCoV-NL63,
      HCoV-OC43, and HCoV-HKU1, circulate globally in an epidemic pattern and
      account for a substantial proportion of common cold cases, particularly in
      infants, the elderly, and immunocompromised individuals.
    explanation: >-
      Establishes the seasonal/epidemic circulation of the four endemic HCoVs and
      their substantial contribution to common cold burden. Evidence source is
      OTHER as this is a review article.
  downstream:
  - target: Lower Respiratory and Complicated Infection
    description: >-
      In vulnerable hosts, endemic coronavirus infection can extend beyond the
      upper airway to cause lower respiratory and complicated disease.

- name: Lower Respiratory and Complicated Infection
  description: >
    Although usually mild, the endemic human coronaviruses can cause lower
    respiratory infection, otitis media, asthma exacerbations, gastroenteritis, and
    occasional systemic complications, particularly in infants, the elderly, and
    patients with comorbidities.
  biological_processes:
  - preferred_term: inflammatory response
    term:
      id: GO:0006954
      label: inflammatory response
    modifier: INCREASED
  locations:
  - preferred_term: lung
    term:
      id: UBERON:0002048
      label: lung
  evidence:
  - reference: PMID:33186086
    reference_title: "Complicating Infections Associated with Common Endemic Human Respiratory Coronaviruses."
    supports: SUPPORT
    evidence_source: OTHER
    snippet: >-
      They also may cause simple and complicated lower respiratory infections,
      otitis media, asthma exacerbations, gastroenteritis, and a few systemic
      complications.
    explanation: >-
      Documents the broader and complicated manifestations beyond the common cold.
      Evidence source is OTHER as this is a review article.
  downstream: []
phenotypes:
- category: Respiratory
  name: Rhinorrhea
  description: >
    Nasal discharge is a hallmark of the common-cold illness caused by endemic
    coronaviruses.
  phenotype_term:
    preferred_term: Rhinorrhea
    term:
      id: HP:0031417
      label: Rhinorrhea
- category: Respiratory
  name: Nasal Congestion
  description: >
    Nasal congestion accompanies endemic coronavirus upper respiratory infection.
  phenotype_term:
    preferred_term: Nasal congestion
    term:
      id: HP:0001742
      label: Nasal congestion
- category: Respiratory
  name: Cough
  description: >
    Cough is a common symptom of endemic coronavirus respiratory infection.
  phenotype_term:
    preferred_term: Cough
    term:
      id: HP:0012735
      label: Cough
- category: Respiratory
  name: Pneumonia
  description: >
    Lower respiratory tract infection including pneumonia can occur in vulnerable
    hosts.
  phenotype_term:
    preferred_term: Pneumonia
    term:
      id: HP:0002090
      label: Pneumonia
  evidence:
  - reference: PMID:33186086
    reference_title: "Complicating Infections Associated with Common Endemic Human Respiratory Coronaviruses."
    supports: SUPPORT
    evidence_source: OTHER
    snippet: >-
      They also may cause simple and complicated lower respiratory infections,
      otitis media, asthma exacerbations, gastroenteritis, and a few systemic
      complications.
    explanation: >-
      Supports lower respiratory tract infection as a possible manifestation.
      Evidence source is OTHER as this is a review article.
- category: Constitutional
  name: Fever
  description: >
    Low-grade fever may accompany endemic coronavirus infection.
  phenotype_term:
    preferred_term: Fever
    term:
      id: HP:0001945
      label: Fever
treatments:
- name: Supportive Care
  description: >
    Management of endemic seasonal coronavirus infection is supportive; no specific
    antiviral therapy or licensed vaccine is currently available.
  treatment_term:
    preferred_term: Supportive Care
    term:
      id: NCIT:C15747
      label: Supportive Care
notes: >
  Created as part of the Respiratory Infections project (Intercept-aligned endemic
  respiratory viruses). Created without a MONDO disease_term id because no usable
  MONDO term exists for endemic/seasonal human coronavirus infection (only an
  obsolete sensitivity term) — flagged for a MONDO term request rather than
  anchored to a too-general parent. Models the four endemic HCoVs (229E, NL63,
  OC43, HKU1) as one entry; conforms to the innate_antiviral_interferon_response
  module. HCoV-NL63 uses the ACE2 receptor (the SARS-CoV-2 receptor), a potential
  future host_directed_antiviral_dependency conformance once receptor-specific
  evidence is curated. The infectious_agent (NCBITaxon) block was omitted at
  creation and the organisms are described in text.
datasets:
- accession: geo:GSE282464
  title: 'Molecular landscape of respiratory infection: A large-scale, multi-centre blood transcriptome dataset'
  description: Respiratory infections pose significant challenges to global health, impacting millions of individuals annually. Understanding the molecular mechanisms underlying the pathogenicity of these infections is crucial for developing effective interventions. RNA sequencing provides insights into a patient’s global transcriptome changes, facilitating the identification of host gene signatures in response to infection and potential therapeutic targets.
  organism:
    preferred_term: human
    term:
      id: NCBITaxon:9606
      label: Homo sapiens
  data_type: BULK_RNA_SEQ
  sample_count: 377
  publication: PMID:40640204
  notes: Identified by GEO DataSets index search for Seasonal Coronavirus Infection (scripts/discover_datasets.py); accession and metadata verified against NCBI E-utilities on 2026-08-01. Title, sample count, and organism are GEO's own values.