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).

Ask OpenScientist

Ask a research question about Seasonal Coronavirus Infection. OpenScientist will conduct autonomous deep research using the Disorder Mechanisms Knowledge Base and PubMed literature (typically 10-30 minutes).

Submitting...

Do not include personal health information in your question. Questions and results are cached in your browser's local storage.

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

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 ↑ INCREASED 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.
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 ↑ INCREASED 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.
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.
●

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.
🦠

Infectious Agent

4
Human coronavirus 229E
An endemic alphacoronavirus that uses aminopeptidase N as its host-cell receptor and circulates seasonally as a cause of the common cold.
HCoV-229E NCBITaxon:11137 NCBI Taxonomy (NCBITaxon)
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."
Names HCoV-229E as one of the four endemic human respiratory coronaviruses that cause this illness.
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."
Confirms HCoV-229E as a seasonal human coronavirus accounting for a substantial share of common cold cases.
Human coronavirus NL63
An endemic alphacoronavirus that, unusually among the seasonal human coronaviruses, uses ACE2 - the SARS-CoV-2 receptor - for cell entry.
HCoV-NL63 NCBITaxon:277944 NCBI Taxonomy (NCBITaxon)
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."
Names HCoV-NL63 as one of the four endemic human respiratory coronaviruses that cause this illness.
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."
Confirms HCoV-NL63 as a seasonal human coronavirus accounting for a substantial share of common cold cases.
Human coronavirus OC43
An endemic betacoronavirus that attaches via 9-O-acetylated sialic acid and is often the most frequently detected of the four seasonal coronaviruses.
HCoV-OC43 NCBITaxon:31631 NCBI Taxonomy (NCBITaxon)
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."
Names HCoV-OC43 as one of the four endemic human respiratory coronaviruses that cause this illness.
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."
Confirms HCoV-OC43 as a seasonal human coronavirus accounting for a substantial share of common cold cases.
Human coronavirus HKU1
An endemic betacoronavirus, the most recently recognised of the four, which like HCoV-OC43 attaches via 9-O-acetylated sialic acid.
HCoV-HKU1 NCBITaxon:290028 NCBI Taxonomy (NCBITaxon)
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."
Names HCoV-HKU1 as one of the four endemic human respiratory coronaviruses that cause this illness.
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."
Confirms HCoV-HKU1 as a seasonal human coronavirus accounting for a substantial share of common cold cases.
↔️

Transmission

1
Household and community transmission between close contacts
The seasonal coronaviruses spread from person to person through close contact, both within households and in the wider community, producing the recurrent winter-dominant epidemics that characterise them.
Show evidence (2 references)
PMID:36350773 SUPPORT Human Clinical
"The estimated weekly household transmission probability was 9% (95% CrI, 6-13) and weekly community acquisition probability was 7% (95% CrI, 5-10)."
Prospective surveillance of 223 households quantifies person-to-person spread of the endemic coronaviruses within households alongside community acquisition.
PMID:36350773 SUPPORT Human Clinical
"Household transmission studies inform how viruses spread among close contacts, but few characterize household transmission of endemic coronaviruses."
Frames the household as the close-contact setting whose transmission this study measures for the endemic coronaviruses.
📊

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
infectious_agent:
- name: Human coronavirus 229E
  infectious_agent_term:
    preferred_term: HCoV-229E
    term:
      id: NCBITaxon:11137
      label: Human coronavirus 229E
  description: >-
    An endemic alphacoronavirus that uses aminopeptidase N as its host-cell
    receptor and circulates seasonally as a cause of the common cold.
  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: >-
      Names HCoV-229E as one of the four endemic human respiratory
      coronaviruses that cause this illness.
  - 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: >-
      Confirms HCoV-229E as a seasonal human coronavirus accounting for a
      substantial share of common cold cases.
- name: Human coronavirus NL63
  infectious_agent_term:
    preferred_term: HCoV-NL63
    term:
      id: NCBITaxon:277944
      label: Human coronavirus NL63
  description: >-
    An endemic alphacoronavirus that, unusually among the seasonal human
    coronaviruses, uses ACE2 - the SARS-CoV-2 receptor - for cell entry.
  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: >-
      Names HCoV-NL63 as one of the four endemic human respiratory
      coronaviruses that cause this illness.
  - 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: >-
      Confirms HCoV-NL63 as a seasonal human coronavirus accounting for a
      substantial share of common cold cases.
- name: Human coronavirus OC43
  infectious_agent_term:
    preferred_term: HCoV-OC43
    term:
      id: NCBITaxon:31631
      label: Human coronavirus OC43
  description: >-
    An endemic betacoronavirus that attaches via 9-O-acetylated sialic acid and
    is often the most frequently detected of the four seasonal coronaviruses.
  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: >-
      Names HCoV-OC43 as one of the four endemic human respiratory
      coronaviruses that cause this illness.
  - 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: >-
      Confirms HCoV-OC43 as a seasonal human coronavirus accounting for a
      substantial share of common cold cases.
- name: Human coronavirus HKU1
  infectious_agent_term:
    preferred_term: HCoV-HKU1
    term:
      id: NCBITaxon:290028
      label: Human coronavirus HKU1
  description: >-
    An endemic betacoronavirus, the most recently recognised of the four, which
    like HCoV-OC43 attaches via 9-O-acetylated sialic acid.
  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: >-
      Names HCoV-HKU1 as one of the four endemic human respiratory
      coronaviruses that cause this illness.
  - 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: >-
      Confirms HCoV-HKU1 as a seasonal human coronavirus accounting for a
      substantial share of common cold cases.
transmission:
- name: Household and community transmission between close contacts
  description: >-
    The seasonal coronaviruses spread from person to person through close contact,
    both within households and in the wider community, producing the recurrent
    winter-dominant epidemics that characterise them.
  evidence:
  - reference: PMID:36350773
    reference_title: Household Transmission Dynamics of Seasonal Human Coronaviruses.
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: >-
      The estimated weekly household transmission probability was 9% (95% CrI,
      6-13) and weekly community acquisition probability was 7% (95% CrI, 5-10).
    explanation: >-
      Prospective surveillance of 223 households quantifies person-to-person
      spread of the endemic coronaviruses within households alongside community
      acquisition.
  - reference: PMID:36350773
    reference_title: Household Transmission Dynamics of Seasonal Human Coronaviruses.
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: >-
      Household transmission studies inform how viruses spread among close
      contacts, but few characterize household transmission of endemic
      coronaviruses.
    explanation: >-
      Frames the household as the close-contact setting whose transmission this
      study measures for the endemic coronaviruses.
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) and transmission blocks
  were backfilled under dismech#10115, with one agent record per endemic HCoV
  species.
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.