Fig. 1

The classification and abundance of coronavirus DVGs based on nanopore direct RNA sequencing. (A) The structures of the BCoV full-length genome and canonical sgmRNAs. (B) The DVGs can be divided into 4 subgroups Δ5’3’DVG, Δ3’DVG, Δ5’DVG and 5’3’ DVG based on whether DVGs contain 5’ and/or 3’ UTR sequence (partial or complete). Note that DVGs may consist of 1, 2 or more than 2 fragments based on the criteria and definitions for the classes as described in the figure legend of Figure S1. Shown here are DVGs with 4 fragments to emphasize that they are recombination products derived from the different portions of the genome including part of ORF1a, ORF1b, S and N genes. The dashed line indicates the truncated genome in DVGs. (C)-(E) Left panel: The relative amounts of total DVGs and canonical sgmRNAs in BCoV-and MHV-A59-infected cells and MHV-A59 infected mice. Right panel: The relative amounts of each classified DVG subgroup and canonical sgmRNA in BCoV-and MHV-A59-infected cells and MHV-A59 infected mice. Panels (C)-(E) show the mean of two biological replicates; error bars indicate the standard deviation