Common RNA replication signals exist among group 2 coronaviruses: evidence for in vivo recombination between animal and human coronavius molecules

Abstract

5' and 3' UTR sequences on the coronavirus genome are known to carry cis-acting elements for DI RNA replication and presumably also virus genome replication. 5' UTR-adjacent coding sequences are also thought to harbor cis-acting elements. Here we have determined the 5' UTR and adjacent 289-nt sequences, and 3' UTR sequences, for six group 2 coronaviruses and have compared them to each other and to three previously reported group 2 members. Extensive regions of highly similar UTR sequences were found but small regions of divergence were also found indicating group 2 coronaviruses could be subdivided into those that are bovine coronavirus (BCoV)-like (BCoV, human respiratory coronavirus-OC43, human enteric coronavirus, porcine hemagglutinating encephalomyelitis virus, and equine coronavirus) and those that are murine hepatitis virus (MHV)-like (A59, 2, and JHM strains of MHV, puffinosis virus, and rat sialodacryoadenitis virus). The 3' UTRs of BCoV and MHV have been previously shown to be interchangeable. Here, a reporter-containing BCoV DI RNA was shown to be replicated by all five BCoV-like helper viruses and by MHV-H2 (a human cell-adapted MHV strain), a representative of the MHV-like subgroup, demonstrating group 2 common 5' and 3' replication signaling elements. BCoV DI RNA, furthermore, acquired the leader of HCoV-OC43 by leader switching, demonstrating for the first time in vivo recombination between animal and human coronavirus molecules. These results indicate that common replication signaling elements exist among group 2 coronaviruses despite a two-cluster pattern within the group and imply there could exist a high potential for recombination among group members.

Genomic characterization of equine coronavirus

“…S1). The bulged stem-loop III (96-115) and IV (189-208) closely resemble the stem-loop III and IV that have been identified as replication signaling elements in bovine coronavirus and other group 2 coronaviruses (Raman and Brian, 2005;Raman et al, 2003;Wu et al, 2003). The 3′ UTR of the ECoV genome comprises 289 nt (30,992) and contains a putative bulged stem-loop structure (nt 30,703-30,770) and a putative pseudoknot structure (30,819) (see Supplementary Fig.…”

Subgenomic messenger RNA amplification in coronaviruses

“…2) to distinguish it from BCoV helper virus sgmRNAs. A 3′-proximal segment within the 301-nt MHV 3′ UTR, nt number 46-156 from the 3′ end [which differs by~60% in sequence from the comparable region in the 288-nt BCoV 3′ UTR (19,20), and which is identified as a hypervariable region among Model for generating sgmRNA (−) strands (dashed gray line) from the viral genome (solid black line) during (−)-strand synthesis. In this model, the coronaviral RdRp pauses at intergenic template-switching donor signals (vertical black bars) and is transferred by a copy-choice mechanism to a highly similar acceptor site near the 5′ end of the genome to copy the 5′-terminal leader.…”

RNA structure analysis of alphacoronavirus terminal genome regions

“…Despite limited sequence identity in the 3 UTRs of the two viruses, replacements of the entire 3 UTR (and specific parts of it) were tolerated, suggesting the presence of conserved structures (rather than sequences) that perform cis-acting functions in betacoronavirus replication (Hsue and Masters, 1997). The conservation of functionally equivalent elements in the 3 (and 5 ) UTR(s) among betacoronavirus genomes was further supported by a study showing that a BCoV-derived reporter DI RNA was efficiently replicated by a range of BCoV-and MHV-related betacoronaviruses (Wu et al, 2003). Interestingly, a possible BSL equivalent was also identified in IBV and other gammacoronaviruses and its functional significance was demonstrated using IBV DI RNA constructs (Dalton et al, 2001).…”