...and most of their genes a completely new to science (meaning they are evolutionarily not related to any other known life form)
Would this then be evidence of abiogenesis occurring more than once, or do you mean something else?
It could be - there is still so much we don't know. I think it's unlikely that life only started once and that everything evolved from that first single cell (seems to Adam and Eve to me). I'm sure life occurred several times, some lineages died out, some combined (like ancient archea and bacteria fusing to become eukaryotes, or modern bacteria swapping plasmids). What ever the truth is, it's probably way more complicated than we think (and ultimately unknowable, it will just be hypotheses and conjecture)
I read a hypothesis that these megaviruses might have once been proper cells, which might explain their large genomes (this doesn't feel right to me as it doesn't explain where their protein coat came from)