Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code

Yinda, Claude Kwe; Ghogomu, Stephen Mbigha; Conceição-Neto, Nádia; Beller, Leen; Deboutte, Ward; Vanhulle, Emiel; Maes, Piet; Van Ranst, Marc; Matthijnssens, Jelle

To find support for the hypothesis that picobirna-like viruses possessing a genome that uses alternative codons, would infect mitochondria, we used a codon usage bias analysis. Briefly, we obtained PBVs, mitoviruses and mitochondria sequences that exhibit different genetic codes (3, 4, 5, 9, 10, 13, 14, 21, and 24 [https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi]) from GenBank. From these sequences, we obtained the codon usage bias using the codon usage tool (Stothard 2000) . We excluded codons that vary between genetic codes and genetic codes for which there is only one sequence (10, 14, 21, and 24) . A list of the accession numbers of the sequences used for PCA is in Supplementary Table S3 . PCA was performed and the figure was created in R (R Core Team 2016) using the built-in stats and ggplot2 (Wickham 2009 ) packages.