yes you would want to know the entire genomic sequence of a virus to target specific parts of the genome and avoid off target effects. when selecting primers and guide RNAs for CRISPR you need to target a unique sequence. the only way to ensure you're targeting a unique sequence is to look in the entire genome.

isolating and sequencing an entire viral genome is not difficult though. it's routine

No.

The gain of function research can be performed with monoclonal isolates, as they are called.

Mainly, they are studying different variants of the S spike protein, which can also be generated in small isolates to study.

The S spike protein can exist is a variety of different shapes. Think of it as a loosely coiled spring and different S spikes are wound tighter than others. Your body produces the CR3022 protein to fight off the S spike. By changing the shape of the spring, slightly, they were hoping to evade the body's defenses.

The CR3023, in your body, is produced on a white blood cell polyprotein chain. In he lab, they do monoclonal isolates... just the piece of interest.

However, the SARS COV 2 S spike turned out to fit too loosely to have any efficacy. This is why the pandemic failed to be an actual pandemic, if you believe SARS COV 2 is even real.

That's a good question.