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Several large viruses (Arslan 2011) form their own organelles within the amoebae they invade.

How do these organelles form?

Reference:

Arslan, D., Legendre, M., Seltzer, V., Abergel, C., Claverie, J-M. (2011) Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae. PNAS 108(42): 17486-17491 [DOI]

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The organelle form in the same way they would if they were coded for by the host's genome, except in this case the virus uses its own genome to specify the type of organelle.

The article you link to indicates this. The "systems" in the quote are in part the organelle that it needs

A study of the giant virus’s DNA shows it to have over a thousand genes, the biochemical instructions it uses to build the systems it requires to replicate once inside its host.

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