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English: RNA synthesis by the flavivirus replication complex. (A) RNA replication by flaviviral NS3 and NS5 proteins. A (+) strand genomic RNA serves as a template to produce (−) strand RNA. The (−) strand RNA exists as a dsRNA intermediate (replicative form). The (−) strand within the dsRNA intermediate is then used as a template for (+) strand RNA synthesis. The dsRNA product is released and recycled for additional (+) strand synthesis. Flavivirus replication is asymmetric, and multiple copies of (+) strand RNA are synthesized from a (−) strand template. The (+) strand RNA is then capped and methylated by NS3 and NS5 to form (+) strand genomic RNA. The identities of the enzymes involved in each step are shown in purple. (B) 5′-RNA cap synthesis by flaviviral NS3 and NS5 proteins. The type 1 cap is formed on (+) strand RNA via the four sequential enzyme activities of RNA triphosphatase, guanylyltransferase, guanine-N7-MTase, and RNA 2′O-MTase. First, triphosphatase activity of the NS3 helicase releases the terminal phosphate from the 5′-triphosphate end of (+) strand RNA. A guanosine monophosphate (GMP) moiety from GTP is transferred to the 5′ end of the now-diphosphorylated RNA through guanylyltransferase activity of the NS5 MTase. The capped RNA is then methylated first at the N7 position of the guanine cap and subsequently at the ribose 2′-O position of the first RNA nucleotide. The MTase domain of NS5 carries out both methylations using S-adenosyl-l-methionine (AdoMet) as a methyl donor. AdoMet is converted to S-adenosyl-l-homosysteine (AdoHcy) during this process.