SubgenomicmRNAs are essentially smaller sections of the original transcribedtemplate strand.

Duringtranscription, the original template strand is usually read from the3' to the5' end from beginning to end. Subgenomic mRNAs are created when transcription begins at the 3' end of the template strand (or 5' of the to-be-newly synthesized template) and begins to copy towards the 5' end of the template strand before "jumping" to the end of the template and copying the last nucleotides of the 5' end of the template, (finishing the 3' tail for the newly created strand).

As a result, the translated strand will have a similar 5' end to varying degrees with the original template (depending on which part of the template the transcription jumped over) and a similar 3' end to the template.^[1]

Positive-sense (5' to 3') viral RNA which may be directly translated into the desired viral proteins, undergoes a similar process as described in 3' to 5'. Portions of the viral RNA may be skipped during translation.

The result is that many differentproteins can be created from the same mRNA strand, with similar 5' ends (to varying degrees) and same 3' ends. Or, different proteins can be created with positive sense viral RNA.

The 5' section on the newly created strand matches that of the template strand, and this section on the template strand is referred to as the "nested set".^[2]

3'                                                          5' GCCGCCCCGTATCGATCGTAGCGCACGTTATATATACGTTATTTCTGCGCGGAAAAAAAAA - Original template Strand 5'                                                          3' GCCGCCCCGTATCGATCGTAGCGCACGTTATATATAC---------------AAAAAAAAA      | GCCGCCCCGTATCGATCGTAGCGCAC--------------------------AAAAAAAAA      | = Subgenomic mRNA.  GCCGCCCCGTAT----------------------------------------AAAAAAAAA      |  GCCGCCCCGTAT = Nested Set  - indicates jumps.

This complex method of transcription is generally restricted toviruses, especially those of the single-stranded, positive-senseRNA or Class IV viruses using theBaltimore Classification System, e.g. viruses of the orderNidovirales.

It is primarily used for compacting moregenetic information into a shorter amount of genetic material.^[3]

• RNA