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Molecular biology techniques are routinely used to diagnose and monitor treatment in patients with chronic hepatitis B (CHB). These tools can detect and quantify viral genomes and analyse their sequences to determine genotype. The increasing use of these tools to monitor patients has greatly improved the management of CHB infection by maximizing the potential for individualized treatment. HBV genotyping has become increasingly important and provides additional information to predict a response to therapy. More sensitive methods to determine HBV DNA levels are now available and the units of measurements have been standardized. HBsAg levels in serum have been shown to reflect active intrahepatic covalently closed circular DNA (cccDNA) and to have additional value in treatment decisions, especially as an on-treatment marker.