Schematic of the cbVG and delVG generation. (A) Standard viral genome replication by the RNA-dependent RNA polymerase (RdRp). (B) Steps of production of a copy-back viral genome (cbVG) during the replication: (1) During synthesis of the nascent strand, the RdRp releases off the template at the break position, then reattaches on the nascent strand at the rejoin position; (2) the RdRp continues synthesis using the nascent strand as template; (3) the RdRp continues elongating the nascent strand; (4) a cbVG molecule containing complementary ends and loop structure is produced. (C) Steps of production of a deletion viral genome (delVG) during the replication: (1) During synthesis of the nascent strand, the RdRp jumps off the template at the break position, then reattaches on a further upstream position on the template strand; (2) the RdRp continues reading the template strand and (3) keeps elongating the nascent strand; (4) a delVG is produced. (D) Representation of the cbVG where the junction region is highlighted by a red box. Gray/white dashed line represents portion of the sequence that is reverse complementary to the gray/black dashed line portion. (E) Representation of the delVG where the junction region is highlighted by a red box.
