. 2010 Feb 6;12(1):62–69. doi: 10.1007/s11894-009-0088-1

Table 2.

Genotypic and phenotypic assays

	Advantages	Disadvantages
Genotypic assays
Direct PCR sequencing	Thorough identification of all mutations	Poor sensitivity (∼ 20%)
Restriction fragment-length polymorphism	Sensitive to ∼ 5%	Requires separate endonuclease reactions for each mutation
Reverse hybridization line probe assay	Sensitive	Requires specific probe for every mutation
Reverse hybridization line probe assay	Commercially available	Requires specific probe for every mutation
DNA microchip	Able to detect new mutations	Expensive
DNA microchip	Able to detect new mutations	Not widely available
Mass spectrometric analysis	Very sensitive	Requires new primer for each mutation
Ultra-deep pyrosequencing	Sensitive to 0.1%	Early in development

Phenotypic assays
Transient transfection with site-specific mutagenesis	Rapid	Not applicable for multiple or complex mutations
Transient transfection with site-specific mutagenesis	Good for single mutations	Not applicable for multiple or complex mutations
Whole HBV genome amplification/cloning and transfection	Whole HBV genome variability	Requires cloning step
Whole HBV genome amplification/cloning and transfection	Cross-resistance testing	Requires cloning step
Cell transduction using Baculovirus vector	High levels of replication	Multiple vectors required
Cell transduction using Baculovirus vector	Cross-resistance testing	Multiple vectors required
Permanent cell lines with expression of HBV mutant genome	Reproducible	New cell line needed for new mutations
Permanent cell lines with expression of HBV mutant genome	Cross-resistance testing	New cell line needed for new mutations

HBV—hepatitis B virus; PCR—polymerase chain reaction