It is commonly noticed that chaotic and inefficient subgenotyping are universally used academically and clinically, a standardized HBV genotype/subgenotype classification criterion is urgently acquired. Sequence similarity, which was commonly used for the last three decades, should be upgraded by phylogenetic analysis in genotyping of recombinant-free HBV strains. In this study, 4,429 HBV whole-genome sequences were employed to reconstruct the phylogeny of HBV using Bayesian inference. After excluding recombinant sequences, calculating partitioned evolutionary models, excluding recombinant sequences, reconstructing phylogenetic trees, and performing a correlation analysis of genetic distances, geographical distribution and serotypes, we systematically redefined the genotypes and subgenotypes of HBV. Compared to previous taxonomy, fourteen subgenotypes (A5-A7; B5-B9; C2-C4, C7; and D6-D7) were revised in the new standard. Now the HBV is divided into ten genotypes (A-J) and 24 subgenotypes (A1-A3; B1-B5; C1-C6; D1-D6; and F1-F4). Our robust genotype/subgenotype new taxonomy has objectively re-molded the current shape of HBV classification. We believe that all future hepatitis B related researches or diagnosis will be benefited under the new HBV genotyping/subgenotyping standards.

GenScalpel is a program designed for the retrieval and extraction of specified sequences from large-scale sequence sets in NCBI GenBank flatfile format. This routine task in bioinformatics analysis is a pressing need for laboratory biologists. Another objective of application development is to respond to the new form of the NCBI Nucleotide Sequence Database, which was updated in November 2011. In addition to a powerful sequence refinement application, GenScalpel provides convenient functions for web-based sequence downloading or multiple files batch processing. This note discusses major applications of the program and includes example data sets to demonstrate its performance. The program is written in PERL. GenScalpel, including installation packages for Windows and Linux systems as well as the accompanying documentation, are available free of charge at http://genscalpel.biosv.com/.

Although transfusion reactions are directly related to transfusion components, transfusion components are clinically related to the diseases afflicting patients. As some transfusion reactions can be life-threatening, estimating the incidence of transfusion reactions (which, in this study, are strictly defined as allergic and febrile non-haemolytic transfusion reactions) of certain categories of diseases is helpful for clinicians. According to the reported blood use of specific departments, the numbers of transfusion patients in these departments can be estimated. By the Association rule mining algorithm, the categories of diseases that often correlate with transfusion reactions have been screened for. It is found that the diseases belonging to C00-C97, D00-D48, D50-D89, K00-K93, N00-N99 and O00-O99 (ICD-10) often correlate with transfusion reactions. Platelet transfusion patients whose diseases belong to C00-C97 encounter transfusion reactions with an incidence of about 1%, which is much higher than the average. The incidence of transfusion reactions in patients whose diseases belong to K00-K93 –who undergo plasma transfusions –might be higher than the average, as the lower bound of this incidence is equivalent to the average incidence. Based on this study, it is suggested that attention be paid to patients whose diseases belong to C00-C97 –who undergo platelet transfusions –to prevent them from experiencing allergic transfusion reactions.