SARS-CoV-2 produces nine subgenomic RNAs (sgRNAs). N protein-encoding mRNA (mRNA9) is most abundantly expressed, followed by mRNAs encoding proteins S (mRNA2), 7a (mRNA7a), 3a (mRNA3), 8 (mRNA8), M (mRNA5), E (mRNA4), 6 (mRNA6) and 7b (mRNA7b) (Kim et al. 2020).

SARS-CoV-1 encodes eight subgenomic RNAs, mRNA2 to mRNA9. mRNA1 corresponds to the genomic RNA. mRNA2 encodes the S protein. mRNA3 is bicistronic and encodes proteins 3a and 3b. mRNA4 encodes the E protein. mRNA5 encodes the M protein. mRNA6 encodes the protein 6. mRNA7, mRNA8 and mRNA9 are bicistronic, with mRNA7 encoding proteins 7a and 7b, mRNA8 encoding proteins 8a and 8b, and mRNA 9 encoding proteins 9a and N. The 5' and 3' ends of subgenomic RNAs are identical, in accordance with the template switch model of coronavirus RNA transcription (Snijder et al. 2003, Thiel et al. 2003, Yount et al. 2003). Based on studies of the murine hepatitis virus (MHV), which is closely related to SARS-CoV-1, positive-sense virus mRNAs are present at much higher amounts than negative-sense mRNAs (Irigoyen et al. 2016).