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Intrahost evolution of HBe antigen-negative hepatitis B virus genomes ascribed to the F genotype: a longitudinal 3 year retrospective study

¹ Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Piso 4, 1113 Buenos Aires, Argentina
² Laboratorio de Hepatitis Virales, Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155, Piso 11, 1121 Buenos Aires, Argentina

Correspondence
José Luis López
jlopez{at}ffyb.uba.ar

The intrahost hepatitis B virus (HBV) genomic evolution process of an HBe antigen (HBeAg)-negative chronic HBV patient (designated RI) was studied. Two nearly full-length direct sequences obtained in 1995 (RI95) and 1998 (RI98) showed: (a) a mutation rate of 2.7x10^–3 nucleotides per site per year; (b) nucleotide changes mainly located at single coding regions (P=0.002); (c) mixed populations; and (d) a predominance of non-synonymous substitutions (P=0.0036). Population heterogeneity was assessed by cloning and sequencing of a fragment spanning nearly half the genome. Two-thirds of the analysed clones exhibited long nucleotide deletions. Pairwise genetic diversity revealed that diversity was higher for RI95 than for RI98 cloned sequences. In conclusion, a highly heterogeneous genomic population circulated within patient RI, which might support the persistence of HBV. Finally, the structure of the deletant genomes suggests that they might serve as intermediates for integration to the host-cell genome.

A diagram of the strategy followed to analyse the HBV genomic evolution within patient RI, nucleotide changes between RI95 and RI98, mapping of deletions within the 13 deletant clones, and mutation distribution for the clone-derived sequences of fragment 1 and RI98 direct sequence with respect to the RI95 direct sequence, are available as supplementary material in JGV Online.