After pondering this question obsessively, I agree with the conclusion that the other respondents find obvious: Jeffrey was not involved in the virus plot. However, my conclusion is based on two pieces of evidence not yet mentioned.
First is a seemingly throw-away line uttered by one of Jeffrey's henchmen in the pivotal scene where Leland Goines has been kidnapped. The henchman jokingly says "if you guys get caught... I've never seen you before in my life." This line feels unnecessary at first, and probably wouldn't fit at all if the henchman was involved in a plot as serious as killing humanity with a virus. But the line would make sense as a way to show the audience that Jeffrey's plot is the much-more-mundane releasing of zoo animals.
Second piece of evidence comes from the following excerpt from the production draft of the script, which made it obvious that Jeffrey did not know of the virus. Of course, in the actual movie, this dialogue is significantly different. But after much deliberation, I'd guess the revision was not intended to change Jeffrey's role, but just to make the reveal less blatantly obvious than originally written here (and that his revised comment "Too late!" was just his insane mind not understanding what his father was talking about):
"Kidnapping Leland Goines" scene as written in production draft of script:
LELAND: I took myself out of the loop! I don't have the code anymore. I don't have access to the virus. So, go ahead -- torture me, but you can't extract anything of use to yourself.
The ACTIVISTS are all exchanging puzzled looks.
LELAND: She knew about it, Jeffrey. She knew you were going to try this.
JEFFREY: What virus are we talking about, Dad?
LELAND: You're insane, Jeffrey.
JEFFREY: You "develop" viruses and you're calling me insane? Typical. What does this virus attack? Don't tell me, you sick fuck, it doesn't matter. (to the others) Have I ever "developed" a virus? Do I put helpless animals in cages and measure their reactions to electrical stimuli? Do I inject radioactive substances into living creatures and examine their bowel movements? Wow! And I'm crazy!
LELAND: Please tell me, Jeffrey, what exactly are you going to do? I don't have to tell you I'm afraid.
JEFFREY: THIS IS A FUCKING EXPERIMENT! YOU'RE OUR HELPLESS LITTLE TEST ANIMAL, DADDY. GOT THAT? NOW -- WHAT FUCKING VIRUS HAVE YOU COME UP WITH, YOU DEMENTED FUCKING MANIAC?
[end of scene]