Coronavirus 5′ UTR

The 5′ UTR is responsible for important biological functions, such as viral replication, transcription[1] and packaging.

The 5′ UTRs are predicted to contain three conserved stem-loops:[3] Downstream of SL4 lies SL5, which overlaps with the first ORF of the viral genome.

[2] Similar to Alphacoronavirus, the first 150 to 200 nucleotides within the Betacoronavirus 5′ UTR are highly structured and contains three conserved stem-loops (SL1, SL2 and SL4).

SARS-CoV and BCoV have an additional stem-loop, called SL3, which contains the TRS-L sequence in its loop region.

SL1 and SL2 have major impacts of the level of viral replication, whereas SL4 is hypothesized to play a role as a "spacer" during the template-switch of sgRNA synthesis.

Consensus secondary structure and sequence conservation of aCoV-5UTR (Rfam RF03116 ).

Consensus secondary structure and sequence conservation of bCoV-5UTR (Rfam RF03117 ). The first 3 helices are SL1, SL2 and SL4 and the last 3 are parts of SL5.

Consensus secondary structure and sequence conservation of dCoV-5UTR (Rfam RF03119 ).