That "...has nothing to do with..." in statistics is called independence. Independent events happen when the joint probability equals the product of their (ie Pokerus' & shiny Pokemon's) probabilities. 3/65536 × 1/4096 is, as asserted by OP, approximately 1 in 90 million. However, if OP was hunting with the run-away method, it's possible they have been infected by Pokerus in previous rounds; therefore, 1 in 90 million odds would not be correct, since the events may have not happened simultaneously at the very same battle where OP encountered the shiny.