The problem is simply observational. We don't even have reliable DNA and RNA sequencing of our own bodies. And we cannot reliably observe things in a host without knowing, to some extent, what we're looking for first. Even that space is so large, it's very hard to ascertain accurately. Biology is always suffering for lack of clear observations.

Also, adding complexity is the difficulty or even literal impossibility of observing the direct interactions of elements of the system, which operate at a quantum scale, that you would disturb and do disturb when attempting to observe.