Detection and quantification
of viral genomes

Detection, generally associated with the quantification of viral genomes (DNA or RNA of the virus), is an essential element for direct diagnosis in virology. Indeed, the presence of the viral genome is an indication of viral multiplication at the site of the targeted organ. The methods of detection and quantification of viral genomes are principally based on amplification of the target (PCR for “polymerase chain reaction” or TMA for “transcription-mediated amplification”) or amplification of the signal (bDNA for “branched DNA”).

Available Biological Analyses

Detection and quantification of viral RNAs and DNAs are realized using automated systems :

ANALYSIS	INDICATION	DEVICE	REAGENTS
Detection/quantification of HBV ADN (quantification of viral load)	Diagnosis and moritoring of chronic hepatitis B Therapeutic follow-up of chronic hepatitis B	GeneXpert	Cepheid ref.MADGXHBV-VL-CE-10
		Cobas	Roche ref.4894570190
		m2000	Abbott ref.2G3490
Detection/quantification of HCV RNA (quantification of viral load)	Diagnosis and moritoring of acute or chronic hepatitis C Therapeutic follow-up of chronic hepatitis C	m2000	Abbott ref.4J8690
		GeneXpert	Cepheid ref.MADGXHCV-VL-CE-10
		Cobas	Roche ref.5532264190
Detection/quantification of HIV RNA (quantification of viral load)	Diagnosis of HIV infection Therapeutic follow-up of HIV infection	Cobas	Roche ref.5212294190
		GeneXpert	Cepheid ref.MADGXHIV-VL-CE-10
Detection/quantification of HEV RNA (quantification of viral load)	Diagnosis and moritoring of acute or chronic hepatitis E	m2000	Altona ref.271013
Detection/quantification of CMV DNA in whole blood (quantification of viral load)	Diagnosis of primary CMV infection Diagnosis of CMV reactivation Therapeutic follow-up of CMV infection	Rotor-Gene Q	Qiagen ref.4503363
Detection/quantification of EBV DNA in whole blood (quantification of viral load)	Diagnosis of EBV reactivation Diagnosis of EBV-associated lymphoproliferation Therapeutic follow-up of EBV infection	Rotor-Gene Q	Qiagen ref.4501363
Detection/quantification of BK virus DNA in urine sample or whole blood (quantification of viral load)	Moritoring of kidney transplant Etiological diagnosis of hemorrhagic cystitis	Rotor-Gene Q	Qiagen ref.4514363
Detection/quantification of HHV-6DNA in whole blood (quantification of viral load)	Etiological diagnosis of fevers or encephalitis of an immunocompromised host	Rotor-Gene Q	Elitech ref.RTS036PLD
Qualitative detection of HSV-1 and HSV-2 DNA	Etiological diagnosis of encephalitis (HSV-1) and meningitis (HSV-2)	StepOnePlus	Biomérieux ref.69-004B
Qualitative detection of VZV DNA	Etiological diagnosis of vesicular legions Etiological diagnosis of viral meningitis	StepOnePlus	Biomerieux ref.69-004B
Qualitative detection of Enterovirus DNA	Etiological diagnosis of viral meningitis	GeneXpert	Cepheid ref.MADGXEV-100N-10
Qualitative detection of HHV-6 DNA except for whole blood (other samples)	Etiological diagnosis of fevers or encephalitis of an immunocompromised host	Rotor-Gene Q	Elitech ref.RTS036PLD
Qualitative detection of HHV-8 DNA	Etiological diagnosis of Kaposi's sarcoma, serous lymphoma, Castleman's disease	Rotor-Gene Q	Elitech ref.RTS038PLD
Qualitative detection of parvorirus B19 DNA	Diagnosis of primary parvovirus B19 infection Etiological diagnosis of anemia in immunocompromised patiens Etiological diagnosis of anemia in patients with hemoglobinopathies	Rotor-Gene Q	Elitech ref.RTS070PLD
Qualitative detection of adenovirus DNA	Etiological diagnosis of gastroenteritis and viral resembling pneumonia Etiological diagnosis of severe infections in immunocompromised patients	StepOnePlus	Biomérieux ref.69-010B
Qualitative detection of zika virus RNA	Etiological diagnosis of a virus from an at-rick area	Rotor-Gene Q	Altona ref.591013
Multiple qualitative detection of genomes of respiratory viruses : respiratory syncytial virus, human metapneumovirus, rhinovirus/enterovirus, adenovirus, coronavirus, parainfluenza, influenza A (H1N1, H3N2) et B viruses	Etiological diagnosis of acute pneumonia	Filmarray	Biomérieux ref. RFIT-ASY-0136
Qualitative detection of influenza A virus RNA (flu)	Etiological diagnosis of acute pneumonia	GeneXpert	Cepheid ref.MADGXFLU/RSV-CE-10
Qualitative detection of influenza B virus RNA (flu)		GeneXpert	Cepheid ref.MADGXFLU/RSV-CE-10
Qualitative detection of respiratory syncytial virus RNA		GeneXpert	Cepheid ref.MADGXFLU/RSV-CE-10
Norovirus qualitative PCR	Suspected viral Gastroenteritis	GeneXpert	Cepheid ref.MADGXNOV-CE-10

Equipment

The Laboratory of Virology is equipped with several automated systems designed to detect and quantify viral genomes:

1 PANTHER real-time PCR extractor/thermocycler (Hologic)

1 COBAS AmpliPrep automatic nucleic acids extractor (Roche Molecular Systems) coupled with 1 COBAS Taqman 96 real-time PCR thermocycler (Roche Molecular Systems)