The question assumes that organisms came before viruses.  From the latest attempts to deduce what happened many years ago, a current belief is that [viruses and organisms had a single originating organism][1].  This means that in terms of the current species, the two likely already were subjects of [Endogenosymbiosis][2], where one didn't necessarily directly come into existence before the other.

Currently most viruses have become so efficient that they lack the means to be remotely organisim-like, depending heavily on their hosts.  But, there are the ancient viruses, [like the pandoravirus, which contain about 2,500 protein encoding regions][3], a number larger than the number of genes in the [smallest of free living organisms (1,400)][4].  These viruses may hint toward the structure of ancient viruses which split from their originating organisms.

This idea of co-evolution of organism and virus might flip the question on its head.  "Is 8% of the DNA in a human cell sourced from human or near-human cells, by way of viruses?"

As for the misnomer "junk" DNA; we're finding out that rates of expression, DNA folding, and other factors that tend to impact the expressed portion invariably are side effects of some of that "junk" DNA.  Instead of the 98% "junk" designation, [the current belief is that about 80% of our DNA is "biochemically active"][5] You certainly wouldn't get the same organism with the misnomered "junk" DNA removed.


  [1]: https://cosmosmagazine.com/biology/what-came-first-cells-or-viruses
  [2]: https://en.wikipedia.org/wiki/Endogenosymbiosis
  [3]: https://en.wikipedia.org/wiki/Pandoravirus
  [4]: http://www.biology-pages.info/G/GenomeSizes.html
  [5]: http://healthland.time.com/2012/09/06/junk-dna-not-so-useless-after-all/