Question

Are there examples of new ORFs in SARS-CoV-2 created by mutations?

The ORFs should not be present in the reference virus, but they should occur in a lineage occurring in the wild (at best, being part of the definition of the lineage). Of course those ORFs will somehow overlap with the well-known ORFs of the virus, potentially frame-shifted.

Bonus: Is there evidence that a protein is produced from the newly emerged ORF?

Answer 1

Mutations in SARS-CoV-2 can create new open reading frames (ORFs), leading to the production of novel proteins, as seen in certain virus lineages like the Alpha variant's ORF9b. These emerging proteins can affect virus behavior, including immune evasion.

Step-by-step explanation:

In SARS-CoV-2, new open reading frames (ORFs) can be created by mutations that arise during the rapid viral replication process. Such newly emerged ORFs are sometimes found in specific lineages of the virus that are spreading in the wild. For instance, a well-documented example is the ORF found in the Alpha variant (B.1.1.7), known as ORF9b. This ORF overlaps with a previously known ORF, leading to the production of an alternative protein that may play a role in the virus's ability to evade immune responses. Although the exact functions of these novel proteins are often unclear at their discovery, studies using techniques like mass spectrometry could confirm the expression of these new proteins within infected cells. The emergence of such novel ORFs exemplifies the mechanisms by which coronaviruses evolve, potentially leading to increased virulence or changes in transmissibility.