Coronavirus transcription resembles high-frequency, similarity-assisted copy-choice RNA recombination, requiring sequence identity between donor and acceptor RNAs and hairpin structures present in the acceptor RNA, in which the TRS-L would act as an acceptor for the cTRS-B donor sequence. Secondary structure analysis of the TRS-L region from transmissible gastroenteritis virus (TGEV) and bovine coronaviruses (BCoV) showed that the CS-L is exposed in the loop of a structured hairpin that is relevant for replication and transcription.