New insights into the evolutionary rate of hepatitis B virus at different biological scales
Journal
Journal of Virology
Journal Volume
89
Journal Issue
7
Pages
3512-3522
Date Issued
2015
Author(s)
Lin Y.-Y.
Liu C.
Chien W.-H.
Wu L.-L.
Tao Y.
Wu D.
Lu X.
Hsieh C.-H.
Abstract
The evolutionary rates of hepatitis B virus (HBV) estimated using contemporary sequences are 102 to 104 times higher than those derived from archaeological and genetic evidence. This discrepancy makes the origin of HBV and the time scale of its spread, both of which are critical for studying the burden of HBV pathogenicity, largely unresolved. To evaluate whether the dual demands (i.e., adaptation within hosts and colonization between hosts) of the viral life cycle affect this conundrum, the HBV quasispecies dynamics within and among hosts from a family consisting of a grandmother, her 5 children, and her 2 granddaughters, all of whom presumably acquired chronic HBV through mother-to-infant transmission, were examined by PCR cloning and next-generation sequencing methods. We found that the evolutionary rate of HBV between hosts was considerably lower than that within hosts. Moreover, the between-host substitution rates of HBV decreased as transmission numbers between individuals increased. Both observations were due primarily to changes at nonsynonymous rather than synonymous sites. There were significantly more multiple substitutions than expected for random mutation processes, and 97% of substitutions were changed from common to rare amino acid residues in the database. Continual switching between colonization and adaptation resulted in a rapid accumulation of mutations at a limited number of positions, which quickly became saturated, whereas substitutions at the remaining regions occurred at a much lower rate. Our study may help to explain the time-dependent HBV substitution rates reported in the literature and provide new insights into the origin of the virus. ? 2015, American Society for Microbiology.
SDGs
Other Subjects
adult; amino acid substitution; Article; clinical article; controlled study; evolutionary adaptation; evolutionary rate; female; gene sequence; genetic distance; genetic drift; genetic variability; hepatitis B; Hepatitis B virus; Hepatitis B virus genotype A; Hepatitis B virus genotype B; Hepatitis B virus genotype C; Hepatitis B virus genotype D; human; male; microbial colonization; natural selection; nonhuman; nucleotide sequence; phylogenetic tree; phylogeny; priority journal; virus genome; virus load; virus mutation; virus transmission; adaptation; aged; chronic hepatitis B; classification; DNA sequence; family health; genetic variation; genetics; Hepatitis B virus; middle aged; molecular evolution; molecular genetics; point mutation; polymerase chain reaction; transmission; vertical transmission; very elderly; virology; Hepatitis B virus; virus DNA; Adaptation, Biological; Adult; Aged; Aged, 80 and over; Amino Acid Substitution; DNA, Viral; Evolution, Molecular; Family Health; Female; Genetic Variation; Hepatitis B virus; Hepatitis B, Chronic; Humans; Infectious Disease Transmission, Vertical; Male; Middle Aged; Molecular Sequence Data; Point Mutation; Polymerase Chain Reaction; Sequence Analysis, DNA
Publisher
American Society for Microbiology
Type
journal article