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Chronic hepatitis B virus (HBV) infection via perinatal transmission is common in the Asia-Pacific region, but related quasispecies (QS) characteristicsare not yet defined. To investigate the homologous, full-length HBV QS after perinatal infection and their clinical implications, five pairs of mother-daughter patients with chronic HBV infection (one patient with liver cirrhosis, one with immune tolerance, and eight with chronic hepatitis) were included. Full-length HBV were amplified by PCR from serum samples before antiviral treatment and cloned; an average of 17 clones per sample were sequenced, and the QS complexities, diversities, and evolution patterns were analyzed. Full-length HBV sequence similarities within mother-daughter pairs were 91.3 to 98.3%. The QS complexities of full-length HBV were similar between mothers and daughters (median of 0.9734 compared to 0.9688, P > 0.05), as were the diversities (median of 3.396 ؋ 10 ؊3 compared to 4.617 ؋ 10 ؊3 substitutions/site, P > 0.05). However, the distribution patterns of QS complexities and diversities within specific genes were different, and QS genetic distances of the mothers were higher than those of daughters, both more evident in pairs with different antiviral responses and different immune phases or stages. The nucleotide substitution rate of full-length HBV was 14.388 ؋ 10 ؊5 substitutions/site/year, whereas the preC/C gene rate was the highest. Mutations and indels were more common in clones from the mothers, which decreased the affinity of epitopes by 6-to 89-fold. The various genes from homologous HBV genomes evolved in different patterns despite numerically comparable full-length QS complexities and diversities. The different patterns may correlate with the immune stages of chronic HBV infection, which warrants further study. C hronic hepatitis B virus (HBV) infection is still a serious public health problem, with potential adverse sequelae, such as liver cirrhosis, liver failure, and hepatocellular carcinoma. More than 350 million people are chronically infected with HBV, and 75% reside in the Asia-Pacific region (1, 2), where the infection is usually acquired perinatally or in early childhood. In contrast to a very short immune-tolerant (IT) phase in adult-acquired chronic HBV infection, the perinatally or early-childhood-acquired chronic HBV infection has a long immune-tolerant phase, followed by an immune-reactive phase, inactive carrier state, HBeAg-negative chronic hepatitis B, and HBsAg-negative phase. The clinical and laboratory characteristics of each phase have been described in detail previously (3, 4).Due to absence of proofreading during reverse transcription and a high replication rate, the HBV population consists of genetically distinct but closely related variants known as quasispecies (QS). QS means a spectrum of mutants that possess different fitness levels in certain environments (5, 6). Mutants with higher fitness levels predominate by competitive replication, and the predominant mutant may differ in a changing environmen...