Novel HCV subtypes

Code and data from:
Mbisa JL, Lapp Z, Bibby DF, Phillips LT, Manso CF, Packer S, Simmons R, Harris K, Mohan J, Chinnappan L, Leitner T, Bradshaw D. Identification of two novel subtypes of hepatitis C virus genotype 8 and a potential new genotype successfully treated with direct acting antivirals. The Journal of Infectious Diseases. 2024 May 8:jiae253.
https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiae253/7667232

Repository contents:

• novel_hcv_subtypes.qmd: Quarto file containing the code used to perform all analyses
• novel_hcv_subtypes.html: rendered Quarto file with figures and summary statistics; to view, download and open in a web browser
• data: directory containing the alignment and phylogeny used for analyses
• figures: directory containing manuscript figures created by running the code in novel_hcv_subtypes.qmd
  • full_tr_mod.pdf is a manually modified version of the tree that more clearly shows that there are 4 8a sequences present
• simplot: directory containing output from SimPlot++ analysis to search for signatures of recombination