Fig. 2.

SARS-CoV-2 expresses a small RNA derived from the ORF7a sequence. (A) Viral small RNA reads obtained from the three cell lines infected with SARS-CoV-2 map to a single distinct peak within the viral genome (data for MOI 5, 24 hpi are shown). The replicates for each cell line were overlayed on a single track (represented by different colors) and are normalized to 10⁷ total reads. (B) The reads coming from SARS-CoV-2 (∼20 to 25 nt long) map near the beginning of the ORF7a gene (encoded amino acids are shown above the nucleotide sequence). Data from Calu-3 cells are shown. (C) CoV2-miR-O7a forms a hairpin with the sequence immediately downstream in the ORF7a transcript. Shaded nucleotides indicate the sequences detected by Northern blot probes: orange for 5p and blue for 3p. (D) CoV2-miR-O7a and its precursor can be detected by Northern blotting of extracts from Calu-3 cells infected with SARS-CoV-2 at MOI 0.05. (E) As measured by custom TaqMan RT-qPCR, CoV2-miR-O7a is present in nasopharyngeal samples from SARS-CoV-2–infected individuals (Right), with its levels correlating with viral load (Left).