Hepatitis B virus (HBV) genomes show a high rate of mutations. This can lead to a variety of amino acid changes in the surface and polymerase genes, causing changes in viral protein conformation that can result in diminished antibody binding or decreased secretion of surface antigen (HBsAg). HBV monitoring increasingly relies on HBsAg detection and quantification, and therefore epidemiological data on HBsAg mutations are needed. We therefore analyzed the frequency of HBsAg mutations possibly influencing the quantification of HBsAg (MUPIQHs) in an unselected patient collective. To this end, we determined the HBV surface and polymerase gene sequences of an unselected patient collective of 237 individuals chronically infected with HBV and analyzed the MUPIQHs in these sequences using three different online HBV sequence analysis tools. We found that 17 or 34% of the patients, depending on the online interpretation algorithm used, harbored MUPIQHs and that MUPIQHs were not significantly associated with the duration of disease, treatment, or HBV genotype. Thus, this study shows that a substantial amount of HBV sequences derived from unselected patients chronically infected with HBV carry MUPIQHs, and therefore the reliability of routine quantitative and qualitative HBsAg tests needs to be reevaluated. The S open reading frame (ORF), which codes for the hepatitis B surface protein (HBsAg), is overlapped by the polymerase (P) gene. Therefore, mutations in the polymerase gene associated with drug resistance can result in changes in the HBV surface protein (4-7). These, and mutations introduced in the S ORF by other mechanisms, can influence virion secretion (3). They can also reduce binding of HBsAg to anti-HbS antibodies (8), particularly when they occur in the so-called "a" determinant in the major hydrophilic loop (MHL) region of the HBsAg, which is the major antibody neutralization determinant of HBsAg (9). Because the interaction between HBsAg and anti-HbS antibodies is also the basis for routine HBV diagnosis and therapy monitoring by quantitative and qualitative detection of HBsAg (1, 10), changes in HBsAg influencing the interaction with antibodies or secretion of virions might have an impact on the results obtained by these diagnostic assays. This is especially relevant since HBsAg quantitative measurements are now discussed as a predictor to guide treatment decisions (11,12).Based on viral genome sequence variability, eight HBV genotypes have been defined by specific mutations and a divergence of Ͼ8% in the whole genome, and they have been labeled A to H (13). The clinical impact of the virus genotype in regard to treatment response, to viral mutation patterns associated with drug resistance, and to MHL mutations is not entirely clear (10).For the rapid online genetic interpretation of HBV sequence data, three internet tools are available free of cost: HIV-grade HBV drug resistance interpretation (DRI), (14), Geno2pheno [HBV] (G2P) (15), and Stanford HBVseq (STAN) (16). All three of these programs have thus f...