Hepatitis B Virus (HBV) Genotype and Subtype Reference Sequences

The files in this dataset support an analysis of hepatitis B virus (HBV) diversity and classification of genotypes and subtypes.We have set out to produce a resource comprising alignments of published full-length HBV genetic sequences for different genotypes. These were downloaded from the Hepatitis B Virus Database (https://hbvdb.ibcp.fr/HBVdb/) in January 2019. The reference sequences we propose in each case are defined as being the closest biological sequence to the consensus for each genotype or subtype, with an associated publication that has the fewest deletions/insertions relative to a typical isolate of the subtype.Nucleotide sequence alignments are all provided in FASTA format. Maximum-likelihood tree files are provided unrooted in Newick format and were generated with RAxML (https://cme.h-its.org/exelixis/software.html).Further details on the study are available in this Biorxiv publication: https://doi.org/10.1101/831891 Uploaded files:1. Alignment of all HBV sequences. Alignment of full-length HBV sequences (n = 6412) downloaded in Jan 2019 from HBVdb, supplemented with 71 sequences belonging to genotype I and to under-represented genotype C and D sequences (in the HBVdb database) that were identified on Genbank.2. Alignment of all HBV sequences (stripped). Alignment of retained sequences (n = 2839) after removal of identical and highly similar sequences (within ≤1% of each other, as assessed by pairwise distance). Sequences with the least amount of ambiguous sites were retained for the analysis.3. Alignment of HBV reference sequences. Alignment of representative reference sequences selected for the HBV genotypes and subtypes. The genotype A strain X02763 (widely used as a numbering reference) and genotype D isolate NC_003977.2 (the current NCBI HBV reference strain) were included in the alignment. A table detailing the accession numbers and associated publications of the selected references is available in this Biorxiv publication: link4. Alignment of HBV genotype reference sequences. Alignment of selected genotype reference sequences, also including the genotype A strain X02763 (widely used as a numbering reference), and genotype D isolate NC_003977.2 (the current NCBI HBV reference strain). A table detailing the accession numbers of the selected references is available in this Biorxiv publication: link5. Maximum likelihood phylogenetic trees for HBV genotypes A-F, H and I. Only three sequences of Genotype G remained after excluding similar sequences and there is only a single known isolate of (putative) genotype J, so they were excluded from the analysis. All trees were generated with 1000 bootstrap replicates.a. All genotypes tree. Tree of all the retained sequences after removal of highly similar sequences (sequences given in alignment 2).b. Genotype A treec. Genotype B treed. Genotype C treee. Genotype D treef. Genotype E treeg. Genotype F treeh. Genotype H treei. Genotype I treej. Reference sequences tree. Tree of representative reference sequences of HBV genotypes and subtypes