Quantitative DNA fragment analysis for detecting low amounts of hepatitis B virus deletion mutants in highly viremic carriers

Many variants of hepatitis B virus (HBV) with deletions in the viral genome have been identified. Some of these variants are indicator or even effecto r of a more severe course of hepatitis. These deletion mutants contribute a variable and sometimes very low proportion to the viral population. For ea rly detection of small amounts of deletion mutants among a large number of wild-type genomes, we applied a new screening method designated quantitativ e fragment analysis (QFA). By QFA the whole viral genome can be scanned for the presence of deletions or insertions of greater than or equal to3 nucle otides representing more than 2% of the viral population. Using QFA we show ed that an often described deletion of 8 nucleotides is packaged in viral c apsids and not a polymerase chain reaction (PCR) artifact, QFA was applied to study the emergence of deletion mutants in a group of 18 pediatric patie nts who had been infected from a common source while being under multidrug cancer chemotherapy, All patients had developed a highly viremic asymptomat ic HBV carrier state, In 3 of these patients 3 different kinds of HBV delet ion mutants were found by QFA: 8 bp deletions within the core promoter, cor e gene deletions from 8 to 86 bp, and large deletions of up to 1,989 bp spa nning the precore/core and the preS/S reading frames. PCR primers that spec ifically amplify deletion variants enabled the detection of additional pati ents harboring the investigated variant.