Respiratory Tract

Pneumonia

Influenza, A, B.
Adenovirus
CMV

Nasal wash, throat, NP, sputum
Throat, NP, sputum
Throat, NP, urine

Upper respiratory
infection

Rhinovirus
RSV
Adenovirus
Parainfluenza
Influenza A, B
Enterovirus

Nasal wash, throat, NP
Nasal wash
Nasal wash, throat, NP
Nasal wash, throat, NP
Nasal wash, throat, NP
Nasal wash, throat, NP

Pharyngitis

HSV
Rhinovirus
Adenovirus
Parainfluenza
Influenza A, B
Enterovirus

Throat, NP
Nasal wash, throat, NP
Nasal wash, throat, NP
Nasal wash, throat, NP
Nasal wash, throat, NP
Nasal wash, throat, NP

Ocular

Conjunctivitis

Adenovirus

Eye swab or secretions

Keratitis, Retinitis

HSV

Eye swab or secretions

Digestive tract

Gastroenteritis

Enterovirus
Adenovirus

Throat, NP, rectal, stool
Throat, NP, rectal, stool

Hepatosplenomegaly

CMV

Throat, NP, urine

Cutaneous and Mucous Membrane

Vesicular

HSV
VZV
Enterovirus

Lesion swab, vesicular fluid
Lesion swab, vesicular fluid
Lesion swab, vesicular fluid
Throat, NP, rectal

Exanthematous

Measles
Enterovirus
Adenovirus
CMV

Throat, NP
Throat, NP, rectal
Throat, NP, rectal
Throat, urine

Central Nervous System

Encephalitis

HSV
VZV

CSF, lesion swab, vesicular fluid
CSF, lesion swab, vesicular fluid

Aseptic meningitis

Enterovirus
HSV

Throat, NP, rectal, CSF
CSF, lesion swab, vesicular fluid

Cardiovascular

Myocarditis

Enterovirus
CMV

Throat, NP, rectal, pericardial fluid
Throat, urine

Genital

HSV

Lesion swab, vesicular fluid

Congenital and
perinatal

CMV
HSV

Urine
Lesion swab, vesicular fluid