If someone is infected with both variants (let’s say within a day or two), what are some of the likely outcomes with respect to the virus “evolution”?
is it most likely that only 1 of the 2 variants survives?
if both survive, is it likely that the 2 strains “mix” with each other to produce a 3rd strain? Obviously 2 viruses don’t have “sex” per se, but I read https://www.cnbc.com/2021/12/05/omicron-variant-may-have-picked-up-a-piece-of-common-cold-virus.html that the omicron strain actually has a gene that is found in the common cold virus.
By what mechanism could that have happened? Somehow a common cold gene got inserted into the virus, or did that just happen by random mutation?
My primary question is by what mechanism would a virus insert a snippet of RNA from another virus into its own RNA?
On further study, I found this link to an OSF preprint which talks about “template switching”. https://osf.io/f7txy/
Here is the text:
This highly mutated Spike variant harbors a novel insertion mutation ins214EPE. Although the position 214 appears to be an insertion hotspot10the EPE insertion in Omicron appears to be novel. Previous analyses of sequences deposited in GISAID suggested that insertions in the SARS-CoV-2 genome likely arise from polymerase slippage or template switching.10,21Template switching is a normal event during RNA synthesis for coronaviruses, as this process is used to generate sub-genomic RNAs (sgRNAs).22,23In this process, also known as copy-choice recombination, the RNA-directed RNA polymerase (RdRp) and the nascent strand dissociate from the template RNA strand and reassociate with a new template (or the same template at a different position), and then RNA synthesis continues. Typically, such recombination involves templates with high sequence similarity (“homologous recombination”), although non-homologous (or “illegitimate”) recombination between dissimilar sequences can also occur.
Could someone boil down the meaning here in simpler terms? For starters, I don’t understand how recombination applies to viruses? Isn’t recombination a DNA process? How does it relate to viral RNA?