I concur with Kristian’s cautionary note as to source for the Omicron insert, that actually seems from the alignment to be GCCAGAAGA (not that highlighted). In the -1 reading frame this would code for ARR, a VERY familiar tripeptide motif to those of us who study proteolytic, especially furin, cleavage sites in lots of viruses.
A near identical version 28621 GCCAGAAGc even appears downstream in the WT SARS-CoV-2 nucleocapsid protein around aa115, albeit out of frame. We have seen transposition of sequence by copy-choice, out of frame, already in SARS-CoV-2, with respect to the N gene. Obviously, in infected cells a lot of independent mRNAs for both of these proteins are being synthesized virtually side-by-side and simultaneously, while host-cell specific mRNAs are being suppressed.
The assertion that Omicron contains this host RNA insert is the kind of thing that can easily go “viral” in the internet sense, with all the usual agenda-driven misinterpretations that have plagued discussion of this virus. While I am a strong proponent of promiscuous copy-choice indels and mutations in Coronaviruses, anything that presents even a whiff of extra-Coronavirus RNA in a variant of concern could only engender yet more public mischief. Even though 17/17 is very suggestive, it contains common codons in multiple frames for common peptide motifs, and may not be all that unique among viral sources. Tread softly on the pedal, would be my opinion.
Bill Gallaher