The coding capacity of SARS-CoV-2

Abstract

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Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic

“…Although not evolutionarily novel, the recently discovered ORF3c (Table 1) (Finkel et al 2020), and between-host comparisons suggest purifying selection (πN/πS=0.22, p=0.0278) ( Table 1). We therefore suggest that the SARS-CoV-2 genome could contain additional undocumented or new OLGs.…”

“…Two time points are represented: (1) 5 hours and (2) 24 hours post infection (hpi), labelled "05hr" and "4hr", respectively, in the SRA data. The FASTQ format reads were mapped to the Wuhan-Hu-1 reference genome using Bowtie2 local alignment (Langmead et al 2019), with a seed length of 20 and up to one mismatch allowed, after substituting the isolate's mutations, as listed in Finkel et al (2020). Mapped reads were then classified by read length and trimmed to the first (5′-end) nucleotide for downstream analyses.…”

“…For this analysis, we did not apply the per-site FDR cutoff, thus a DAF=0 is equivalent to the absence of reads mapped to the mutation, after reads are filtered by sequence quality, mapping quality, and LoFreq's default significance threshold (p=0.01). A shorter version of ORF3d that excludes its first 24 codons, where the majority of premature STOP codons in SARS-CoV-2 are located; contains a predicted signal peptide (Finkel et al 2020); likely expressed at higher levels than full-length ORF3d (Figure 2A) a Genes are listed by position of start site in the genome from 5′ (top) to 3′ (bottom).…”

“…Ribosome profiling (Ribo-seq) data were obtained from Finkel et al (2020); mass spectrometry data were obtained from Davidson et al (2020) and Bezstarosti et al (2020). Reads were trimmed to their first (5′) nucleotide to minimize statistical dependence while preserving reading frame.…”

“…Genes are denoted by shape and ordinally colored by iBAQ prop from high (red) to low (blue). 'Upstream peak' refers to the maximum read depth observed at the approximate P-site offset (red bars in Figure 2A), while mean read depths were measured across each gene using 30 nt reads separately for in-frame (codon position 1) and out-of- Figure 2C, except results are shown separately after pooling the two biological replicates for each treatment (CHX=cycloheximide, Harr=harringtonine, LTM=lactimidomycin, mRNA=RNA-seq) (Finkel et al 2020). Genes and their reading frames are denoted by color according to Figure 1, with Frames 1, 2, and 3 corresponding to the frames beginning at codon positions 1, 2, and 3 of ORF3a, respectively.…”