Evidence for quasispecies distributions in the human hepatitis A virus genome.
Nucleotide sequence analysis of multiple molecular clones of the hepatitis A virus (HAV), generated by reverse transcription-PCR of two capsid-coding regions, revealed a degree of heterogeneity compatible with a quasispecies structure in three clinical samples. Passage of plaque-purified reference strain HAV pHM175 43c in FRhK-4 cells documented the generation of a mutant distribution of HAV genomes. The mutant spectra showed mutation frequencies in the range of 1 x 10(-3) to 1 x 10(-4) substitutions per nucleotide, with a dominance of transition over transversion mutations. While in the VP3-coding region, nonsynonymous mutations were predominant; in the VP1-coding region they were uncommon. Around 50% of the amino acid replacements involved residues located at or near antigenic sites. Most of the detected mutations occurred at or in the vicinity of rare codons, suggesting a dynamics of mutation-selection, predominantly at and around rare codons. The results indicate that despite antigenic conservation, HAV replicates as a complex distribution of mutants, a feature of viral quasispecies.
Sánchez
Glòria
G
Grup Virus Entèrics, Department of Microbiology, University of Barcelona, 08028 Barcelona, Spain.
Bosch
Albert
A
Gómez-Mariano
Gema
G
Domingo
Esteban
E
Pintó
Rosa M
RM
D000595:Amino Acid Sequence; D002460:Cell Line; D003062:Codon; D014644:Genetic Variation; D016679:Genome, Viral; D006506:Hepatitis A / Q000821:virology*; D017957:Hepatitis A Virus, Human / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation; D017422:Sequence Analysis, DNA; D012692:Serial Passage; D014764:Viral Proteins / Q000235:genetics; D015678:Viral Structural Proteins / Q000235:genetics
D003062:Codon; C096539:VP1 protein, hepatitis A virus; D014764:Viral Proteins; D015678:Viral Structural Proteins