title: Universal primers for HBV genome DNA amplification across subtypes: a case study for designing more effective viral primers.
abstract: BACKGROUND
  The highly heterogenic characteristic of viruses is the major obstacle to efficient DNA amplification. Taking advantage of the large number of virus DNA sequences in public databases to select conserved sites for primer design is an optimal way to tackle the difficulties in virus genome amplification.
  
  
  RESULTS
  Here we use hepatitis B virus as an example to introduce a simple and efficient way for virus primer design. Based on the alignment of HBV sequences in public databases and a program BxB in Perl script, our method selected several optimal sites for HBV primer design. Polymerase chain reaction showed that compared with the success rate of the most popular primers for whole genome amplification of HBV, one set of primers for full length genome amplification and four sets of walking primers showed significant improvement. These newly designed primers are suitable for most subtypes of HBV.
  
  
  CONCLUSIONS
  Researchers can extend the method described here to design universal or subtype specific primers for various types of viruses. The BxB program based on multiple sequence alignment not only can be used as a separate tool but also can be integrated in any open source primer design software to select conserved regions for primer design.
authors: Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China. zhangqr@big.ac.cn
authors: Qingrun
authors: Q
authors: Zhang
authors: Guanghua
authors: G
authors: Wu
authors: Elliott
authors: E
authors: Richards
authors: Shan'gang
authors: S
authors: Jia
authors: Changqing
authors: C
authors: Zeng
mesh_terms: D017931:DNA Primers; D016679:Genome, Viral; D006515:Hepatitis B virus / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods*; D012984:Software
chemical_list: D017931:DNA Primers