I'd say that it's fairly certain that our reality is ruled by both top-down and down-up causation and I'd be inclined to think that the macro-scale order emerges as a result of intrinsic properties of the quantum fields(i view all the laws of physics as essential inherent properties of the quantum fields that in certain occasions manifest as 'particles' and physical objects). So, in this respect, emergent properties(top down causation) are probably also an inherent component of the quantum fields as well(though they seem like true magic from our point of view). Clearly, our world is mostly what it is because of interactions at the quantum scale(plus a bit of oddity and illusion on part of consciousness). The concepts of space, time and continuos motion aren't really what they appear to be at our scale. In fact, this contradiction is not just in minor details but is quite fundamental, because quantum mechanics requires reality to be discontinuous, noncausal, and nonlocal, whereas relativity theory requires reality to be continuous, causal, and local. This oddity can be patched up in a few cases using mathematical renormalisation, but this approach is awkward and is very likely to be replaced when we have a theory of quantum gravity that would tell us more about the nature of space. What does this have to do with your question? If you can picture the true nature of reality as the water in the ocean, if you gaze at it, at some point our world would appear as appearances of figures and objects in the chaos of the moving waters. And out of this 'quantum soup' appears a totally deterministic orderly world that follows Newton's laws. But peep a bit to left or right, and you'll see the chaos raging. Clearly, cause-effect determinism is mostly a macroscopic manifestation, and our perceived world is mostly deterministic. But so are the quantum partcles that make up our world, they obey the deterministic Schroedinger equation. If anything can challenge this - it would be emergent properties like consciousness and the idea of associated free will.
This is so, for at least 99.9999999999999% of the cases where random quantum events are concerned. But that is so because of the sheer size of the concepts we deal with. The wavefunction of your body seeps slightly around you into space, but because of the number of quanta involved, most of them end up where you normally expect yourself to be. While your chances of suddenly moving non-locally from A to C is 1 to 1 billion trillion or more, for a virus consisting of thousands of atoms, the chances are significantly higher(still nowhere high as we normally apply this category).