My daughter is 2 1/2, and started going through something similar a few months ago; I have heard many other moms say that part of the "terrible twos" is a sudden inability to sleep through the night. Maybe your child is ahead of the curve?
When you say you use the CIO method, do you just leave him to cry it out, or do you use the Ferber style, where you visit him after 3 minutes, and then 5 after that, and then 7 after that, and so on? We have gone back to it, and it helps, really. It takes three days to get established, but it helps.
Also, being sick may have disrupted his routine a bit. You have to start a routine over from scratch every time a major disruption (moving, jet-lag, illness) happens.
Plus, at sixteen months, how many naps is he taking? Cut it down to one. Also, wake him at the same time every morning regardless of how long he's been up at night.
I got (and have used!) all this from the Ferber book, "Solve Your Child's Sleep Problems." I know Ferber has a bad rep w/ some people, but it's been a life saver at our house. Happier parents and happier baby.
Also, I know that many moms don't like medicating their kids, but we found that a dose of infant Tylenol before bed really helped w/ sleeping during teething.
Good luck, momma! Hang in there.