title: Identification of optimal target gene regions for hepatitis B virus genotyping by DNA sequencing.
abstract: OBJECTIVE
  DNA sequencing is the gold standard for hepatitis B virus (HBV) genotyping. We investigated the intergenotypic discriminatory capabilities of various target gene regions over the entire HBV genome, introducing a novel data evaluation approach generally applicable in viral genotyping.
  
  
  METHODS
  Complete genome sequences of seventy HBV variants obtained from the sera of 50 Syrian patients were determined and assigned GenBank accession No. from JN257148 to JN257217. Nucleotide sequence contigs were analyzed together with the NCBI reference genome set of HBV genotypes. Nine target gene regions were analyzed by phylogenetic and scored BLAST analyses. Thirty-one overlapping 300-bp sequence segments over the entire genome were also analyzed using a scored BLAST analysis, and intergenotypic discriminatory capabilities were statistically estimated for each.
  
  
  RESULTS
  Intergenotype discrimination was extremely significant when targeting either the complete genome, the entire coding sequence of either P or S genes, or any 300-bp sequence segment over the coding sequences of S protein or the polymerase N-terminal domain. Interestingly, intergenotypic discriminatory capability correlated negatively with intragenotype variation.
  
  
  CONCLUSIONS
  The intragenotypic conservation of certain target gene regions determines the intergenotypic discriminatory capability and allows reliable genotyping with relatively short segments. Our referential genome-wide tabulated guide allows for selecting candidate target gene regions for sequencing-based HBV genotyping. © 2013 S. Karger AG, Basel.
authors: Clinical Laboratories Department, Al-Assad Hospital, Damascus University, Damascus, Syria. wafahabbal@hotmail.com
authors: W
authors: W
authors: Habbal
authors: B C
authors: BC
authors: Gärtner
authors: F
authors: F
authors: Monem
mesh_terms: D016000:Cluster Analysis; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D016679:Genome, Viral; D006515:Hepatitis B virus / Q000145:classification* / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D058889:Molecular Typing / Q000379:methods*; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D017385:Sequence Homology; D013593:Syria; D014773:Virology / Q000379:methods*
chemical_list: D004279:DNA, Viral