title: Computational evolutionary analysis of the overlapped surface (S) and polymerase (P) region in hepatitis B virus indicates the spacer domain in P is crucial for survival.
abstract: BACKGROUND
  The Hepatitis B Virus (HBV) genome contains four ORFs, S (surface), P (polymerase), C (core) and X. S is completely overlapped by P and as a consequence the overlapping region is subject to distinctive evolutionary constraints compared to the remainder of the genome. Specifically, a non-synonymous substitution in one coding frame may produce a synonymous substitution in the alternative frame, suggesting a possible conflict between requirements for diversifying and purifying forces. To examine how these contrasting requirements are balanced within this region, we investigated the relationship amongst positive selection sites, conserved regions, epitopes and elements of protein structure to consider how HBV balances the contrasting evolutionary pressures.
  
  
  RESULTS
  323 HBV genotype D genome sequences were collected and analyzed to identify sites under positive selection and highly conserved regions. Epitopes sequences were retrieved from previously published experimental studies stored in the Immune Epitope Database. Predicted secondary structures were used to investigate the association between structure and conservation. Entropy was used as a measure of conservation and bivariate logistic regression was used to investigate the relationship between positive selection/conserved sites and epitope/secondary structure regions. Our results indicate: (i) conservation in S is primarily dictated by α-helix elements in the protein structure, (ii) variable residues are mainly located in PreS, the major hydrophilic region (MHR) and the C-terminus, (iii) epitopes in S, which are directly targeted by the host immune system, are significantly associated with sites under positive selection.
  
  
  CONCLUSIONS
  The highly variable spacer domain in P, which corresponds to PreS in S, appears to act as a harbor for the accumulation of mutations that can provide flexibility for conformational changes and responding to immune pressure.
authors.affiliation: Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.
authors.forename: Ping
authors.initials: P
authors.lastname: Chen
authors.forename: Yun
authors.initials: Y
authors.lastname: Gan
authors.forename: Na
authors.initials: N
authors.lastname: Han
authors.forename: Wei
authors.initials: W
authors.lastname: Fang
authors.forename: Jiafu
authors.initials: J
authors.lastname: Li
authors.forename: Fei
authors.initials: F
authors.lastname: Zhao
authors.forename: Kanghong
authors.initials: K
authors.lastname: Hu
authors.forename: Simon
authors.initials: S
authors.lastname: Rayner
mesh_terms: D019295:Computational Biology; D017124:Conserved Sequence; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D000939:Epitopes / Q000235:genetics; D019143:Evolution, Molecular; D016679:Genome, Viral / Q000235:genetics*; D006515:Hepatitis B virus / Q000201:enzymology / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D006801:Humans; D050296:Microbial Viability; D008958:Models, Molecular; D016366:Open Reading Frames / Q000235:genetics; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012194:RNA-Directed DNA Polymerase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012641:Selection, Genetic; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D000939:Epitopes; D014764:Viral Proteins; D012194:RNA-Directed DNA Polymerase; D004259:DNA-Directed DNA Polymerase