Paper HBV Greenland

Repository for the paper "Analysis of Hepatitis B virus genotype D in Greenland suggests presence of novel quasi-subgenotype"

Alignment files

Dataset 1 - Dataset1_HBV.fasta

Dataset 1.1 (subset) - Dataset1.1_HBV_completegenomes.tree

Dataset 1.2 (subset) - Dataset1.2_HBV_900subset_D1_D2_Greenland.fasta

Dataset 2 - Dataset2_HBV_D_GLaDated_wTaiAb.fasta

Dataset 2 (subset unique patients) - Dataset2_HBV_D_GLaDated_wTaiAb_uniquePatients.fasta

Dataset 2 (subset unique patients/full genomes only) - Dataset2_HBV_D_GLaDated_wTaiAb_unique_full_genome_Patients.fasta

GenBank flatfile

Novel Greenland Sequences - HBV_Greenland_new_sequences.gb

Metadata file

Dataset 2 - Dataset2_HBVD_GL_metadata.csv

Recombination analysis files (RDP)

Dataset 2 - Dataset2_HBV_D_GLaDated_wTaiAb.rdp

Phylogenetic tree files

Dataset 1 - Genotype analysis Maximum-Likelihood Tree - Dataset1_HBV_ML_IQTree.tree

Dataset 1.1 - Genotype analysis Maximum-Likelihood Tree - Dataset1.1_HBV_ML_IQTree.tree

Dataset 2 - Maximum Clade Credibility Tree - Dataset2_HBV_D_GLaDated_wTaiAb93_URLSkyride.combined.MCC.tree

Dataset 2 - BEAST XML file - Dataset2_HBV_D_GLaDated_wTaiAb93_URLSkyride.xml

Dataset 2 (subset unique patients) - Maximum-Likelihood Tree - Dataset2_unique_patients.tree

Dataset 2 (subset unique patients/full genomes only) - Maximum-Likelihood Tree - Dataset2_unique_patients_full_genome.tree

Genetic distance

Dataset 1.2 - MEGA X Output - Dataset1.2_HBV_900subset_MEGAoutput_betweengroupmeandistance.xlsx

Authors

Adriano de Bernardi Schneider,
Carla Osiowy,
Reilly Hostager,
Henrik Krarup,
Malene Børresen,
Yasuhito Tanaka,
Taylor Morriseau,
Joel O. Wertheim.

How To Cite

Text Citation:

de Bernardi Schneider, A., Hostager, R., Krarup, H., Borresen, M., Tanaka, Y., Morriseau, T., ... & Wertheim, J. O. (2020). Analysis of Hepatitis B virus genotype D in Greenland suggests presence of a novel subgenotype. medRxiv.

BibTex Citation:

@article{de2020analysis,
  title={Analysis of Hepatitis B virus genotype D in Greenland suggests presence of a novel subgenotype},
  author={de Bernardi Schneider, Adriano and Hostager, Reilly and Krarup, Henrik and Borresen, Malene and Tanaka, Yasuhito and Morriseau, Taylor and Osiowy, Carla and Wertheim, Joel O},
  journal={medRxiv},
  year={2020},
  publisher={Cold Spring Harbor Laboratory Press}
}

Note: OLD folder contains the supplementary files of the original analyses (prior to the last round of peer review).