Table of Contents
Overview – URTI Pathogens and Clinical Syndromes
Upper respiratory tract infections (URTIs) are among the most common presentations in both general practice and paediatrics. This page summarises key URTI pathogens by their preferred anatomical location (from the nasopharynx to the bronchi) and highlights the clinical syndromes associated with each. Also included is a rapid-reference guide to help differentiate between overlapping presentations such as EBV, influenza, croup, and epiglottitis.
Pathogens by Respiratory Tract Location
Nasopharynx
- Rhinovirus
- Adenovirus
- Coronavirus
- RSV (Respiratory Syncytial Virus)
- Influenza Virus
Sinuses & Ears
- Streptococcus pneumoniae
- Haemophilus influenzae
- Staphylococcus aureus
- Moraxella catarrhalis
Oropharynx
- Adenovirus
- Rhinovirus
- Epstein–Barr Virus (EBV)
- Group A β-haemolytic Streptococcus (GABHS)
Epiglottis
Trachea & Bronchi
- RSV
- Rhinovirus
- Coronavirus
- Adenovirus
- Parainfluenza virus
- Influenza virus
- Streptococcus pneumoniae
- Haemophilus influenzae
Lower Respiratory Tract (Note: not technically URTI)
- Streptococcus pneumoniae
- Haemophilus influenzae
- Staphylococcus aureus
- Mycoplasma pneumoniae
- Chlamydia pneumoniae
- (Pseudomonas)
- (Klebsiella)
Common Viral URTI Pathogens
Rhinovirus
- Most common cause of common cold
- Localised to URT; rarely systemic
- Many serotypes → No cross-protection → Repeated infections
- Incubation: 2–3 days
- Symptoms: Nasal congestion, sneezing, sore throat
- Course: Self-limiting, resolved by immune system
Adenovirus
- Common in young children (<5 years)
- Mild URTI: nasal congestion, cough, pharyngitis
- Rarely causes severe disease
Coronavirus
- Includes common cold viruses and SARS-CoV types
- Infects URT and LRT
- Confined to epithelial replication
- Typically mild URTI symptoms
Coxsackie A Virus
- Often causes herpangina or hand, foot, and mouth disease
- May mimic viral pharyngitis
Influenza (Orthomyxoviruses)
- Short incubation: 2–3 days
- Abrupt onset: fever, chills, myalgia, headache
- Complications: pneumonia (esp. elderly and infants), secondary bacterial infections
- Vaccine available; recommended >6 months old
Parainfluenza Virus
- Common in preschool-aged children
- Often causes croup (laryngotracheobronchitis)
- Transmission via respiratory secretions (e.g. shared toys)
- Can be asymptomatic or cause necrotising bronchiolitis
- Diagnosis: Viral culture or RT-PCR
RSV (Respiratory Syncytial Virus)
- Major cause of bronchiolitis in infants
- Highly contagious via secretions
- Forms syncytia (fused respiratory cells)
- Within 24h: rapid progression → cyanosis, respiratory distress
- Reinfection common throughout life
Clinical Syndromes – How to Differentiate URTIs
| Patient Profile | Key Symptoms | Likely Cause |
|---|---|---|
| Adolescent + sore throat + lymphadenopathy | Fatigue, fever, pharyngitis, cervical nodes | EBV (Infectious Mononucleosis) |
| Toddler + drooling + airway distress | Fever, dysphagia, muffled voice, stridor | Epiglottitis (HiB) |
| Toddler + barking cough + stridor | Inspiratory stridor, seal-like cough | Croup (Parainfluenza or RSV) |
| Older adult + T2DM | Subacute presentation, mild symptoms | Atypical pneumonia (Mycoplasma, Chlamydia) |
| Rash + myalgia | Viral prodrome with systemic symptoms | Non-specific viral infection |
| Photophobia + rash + neck stiffness | Meningism, purpuric rash | Meningitis (e.g. Neisseria meningitidis) |
| Pharyngitis → arthritis + murmur after 2 weeks | Fever, polyarthritis, new murmur | GABHS → Rheumatic Fever |
| Recurrent pneumonia + SOB | Poor growth, chronic cough | Cystic Fibrosis / Immunodeficiency |
| SOB + weight loss | Night sweats, haemoptysis, cachexia | Tuberculosis (Mycobacterium tuberculosis) |
| Cough + travel + outbreak context | Recent travel, contact history | SARS / MERS (Coronavirus) |
Summary – URTI Pathogens and Syndromes
Upper respiratory tract infections are caused by a range of viruses and bacteria, many with site-specific preferences. Rhinovirus, coronavirus, and RSV dominate nasopharyngeal infections, while GABHS, EBV, and influenza contribute to oropharyngeal and systemic syndromes. Clinical differentiation depends on age, symptom clustering, and epidemiological context. Knowing which pathogen tends to infect which part of the airway is a high-yield way to orient diagnosis and treatment. For more respiratory topics, see our Respiratory Overview page.