Table 2.: Main Viruses, Samples and Molecular Techniques Used for Viral Diagnosis

Viruses Samples Techniques Infections
CMV CSF Conventional qualitative PCR CNS infection
Blood Real time quantitative PCR Congenital infection
Hybrid capture assay CMV immunosuppressed infections
HSV CSF Nested PCR Meningo-encephalitis
Blood Multiplex PCR Neonatal herpes infection
Leucocytes Hybrid capture assay Generalized and visceral herpes infection in immunosuppressed patients
Specimens from genital ulcers or muco-cutaneous lesions Conventional qualitative PCR
Real time quantitative PCR Dermal and genital diseases
VZV CSF Real time quantitative PCR CNS infection
Exudate from skin lesions Multiplex PCR Cutaneous lesions
Broncho-alveolar lavage Pulmonary infections
Amniotic fluid Congenital and neonatal infections
EBV CSF Conventional qualitative PCR Infectious mononucleosis
Blood In situ hybridization Encephalitis
Lymphocytes Real time quantitative PCR Tumors
Tissue NASBA, Southern blot, dot blot
Parvovirus B19 Blood Conventional qualitative PCR Perinatal and neonatal infections
Bone marrow Real time quantitative PCR
Placental and fetal tissue
Amniotic fluid
Polyomavirus JC CSF Conventional qualitative PCR Leukoencephalopathy
Real time quantitative PCR
Polyomavirus BK Urine Conventional qualitative PCR Nephropathy
Blood samples Real time quantitative PCR
Influenza and parainfluenza viruses Respiratory samples RT-PCR Flu
Real time quantitative PCR Bronchiolitis
Multiplex PCR Croup
Microarrays Pneumonia
Adenovirus Several clinical samples Conventional qualitative PCR Respiratory infections
Real time quantitative PCR Ocular infections
Gastrointestinal infections
Enterovirus CSF RT-PCR CNS infection
Real time quantitative PCR
HPV Cervical exudates and biopsies Type-specific PCR Cervical lesions
Warts biopsies General primers PCR Warts
Other biopsies Liquid hybridization
HPV mRNA detection
Microarrays
Hepatitis viruses Serum or plasma Real time quantitative PCR Chronic infections (viral load)
Liver tissue Hybridization Genotyping
Sequencing
HIV Plasma Real time quantitative PCR Viral load detection

CMV: cytomegalovirus; CSF: cerebrospinal fluid; PCR: polymerase chain reaction; CNS: central nervous system; HSV: virus herpes simplex; VZV: virus varicella-zoster; EBV: virus Epstein-Barr; NASBA: nucleic acid sequence-based amplification; HPV: human papillomavirus; HIV: human immunodeficiency virus; RNA: ribonucleic acid.