(1) No, it would not be idiomatic to insert "as".
(2) a) "I was found to have been infected by a strain of H5N1" ] This makes H5N1 sound like the agent of infection, instead of the infection itself. Cf. "I was slapped by a large Uruguayan", where the Uruguayan is the agent.
However, "infected by" is quite common among native speakers, in such contexts.
(2) b) "I was found to have been infected with a strain of H5N1" ] This seems like the normal version, to me.
(3) "This could be set off" sounds a little strange here; did you mean "this could set off another influenza epidemic"?
(4) Here, we have several occasions. We want to specify that something happens on every one of those occasions. Thus "...each time the virus mutates..."
(Also, "the time the virus mutates" wouldn't be idiomatic!)
(5) I find both "no exceptions" and "no wonder" a little strange. "Without exception" might work.
(6) "the trend that the virus...hasn't yet developed" makes "trend" the object of "develop". But it wouldn't make sense to say that a virus had developed a trend.