This COVID-19 pathway has been created by a combination of computational inference from SARS-CoV-1 data (https://reactome.org/documentation/inferred-events) and manual curation, as described in the summation for the overall SARS-CoV-2 infection pathway. Specifically, binding of the replication-transcription complex (RTC) to the RNA template and the polymerase activity of nsp12 (Hillen et al. 2020, Wang et al. 2020, Yin et al. 2020), helicase activity of nsp13 (Chen et al. 2020, Ji et al. 2020, Shu et al. 2020), capping activity of nsp16 (Viswanathan et al. 2020), and polyadenylation of SARS-CoV-2 genomic RNA and transcripts (Kim et al. 2020, Ravindra et al. 2020) have been studied directly, and the remaining steps have been inferred from previous studies in SARS-CoV-1 and related coronaviruses.
Using the genomic RNA as a template, the coronavirus replicase synthesizes full-length negative-sense antigenome, which in turn serves as a template for the synthesis of new genomic RNA (Masters 2006). The polymerase can also switch template during discontinuous transcription of the genome at specific sites called transcription-regulated sequences, thereby producing a 5'-nested set of negative-sense sgRNAs, which are used as templates for the synthesis of a 3'-nested set of positive-sense sgRNAs (Masters 2006). Although genome replication/transcription is mainly mediated by the viral replicase and confines in the RTC, the involvement of various additional viral and host factors has been implicated. For instance, coronavirus N protein is known to serve as an RNA chaperone and facilitate template switching (Zúñiga et al. 2007, Zúñiga et al. 2010). Importantly, the N protein of SARS-CoV-1 and mouse hepatitis virus (MHV-JHM) is also phosphorylated by the host glycogen synthase kinase 3 (GSK3), and inhibition of GSK3 was shown to inhibit viral replication in Vero E6 cells infected with SARS-CoV-1 (Wu et al. 2009). Additionally, GSK3-mediated phosphorylation of the MHV-JHM N protein recruits an RNA-binding protein DEAD-box helicase 1 (DDX1), which facilitates template read-through, favoring the synthesis of genomic RNA and longer sgRNAs (Wu et al. 2014). Another RNA-binding protein called heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) can also bind tightly to SARS-CoV-1 N protein and potentially regulate viral RNA synthesis (Luo et al. 2005). Host RNA-binding proteins could also bind directly to untranslated regions (UTRs) of the coronavirus genome to modulate replication/transcription, such as zinc finger CCHC-type and RNA-binding motif 1 (ZCRB1) binding to the 5-UTR of IBV (Tan et al. 2012), mitochondrial aconitase binding to the 3' UTR of MHV (Nanda and Leibowitz 2001), and poly(A)-binding protein (PABP) to the poly(A) tail of bovine coronavirus (Spagnolo and Hogue 2000). For review, please refer to Snijder et al. 2016 and Fung and Liu 2019.