HEPA filters remove  a relatively large fraction of particulates, depending on the grade they usually remove, in reality, 90 to 99 percent.  However what matters most for the ability of an air purifier to clean the air in a room is the CADR, the Clean Air Delivery Rate.  Because the air exiting the machine is instantly mixed with the other room air, there is actually no point in stressing over the actual cleanliness of the air exiting the machine.

What matters is the equivalent amount of fully clean air the machine produces.  Another way to think of this is how much particulates the machine removes from the air per minute.  Clearly, if you have say 100 Cubic feet per minute with 80 percent particulate removal, that's equivalent to 80 cubic feet per minute of completely clean air, plus 20 that is unaffected.  This is what CADR measures.

There are several different CADR measures, because filter efficiency is different for different particle sizes, and to an even lesser degree, the type of particle.

Some people think that large amounts of smaller particles can get through filters that are not HEPA. This is actually not true.  Air filtration is not like mechanical sieving, in which particles smaller than the holes in the sieve can get through.  Water filtration is mostly like that.  Air filtration is not.  In air filtration electrostatic forces are very important, and smaller particles are captured by the filter through these kinds of forces attracting them to the fibers of the filter media.  The very small particles are removed very effectively, actually, because the charge to size ratio tends to result in comparatively more effect on their motion and capture by the filter. 

MERV-13 filters, as used in the BQAP, remove about 80-85% of particles in standard tests, in the size range where viruses and bacteria arise.  However at lower airflow velocities we have reason to believe the efficiency may be higher in this particle range.  This remains to be confirmed, but community members have conducted tests that indicate efficiencies in the 99% range.  Thus, MERV-13 filters in this context are nearly the same as even the higher grade of HEPA filters.

You can also get MERV-16 or even HEPA filters in the same size and shape as the 20 by 25 by 1 inch filters typically used in a BQAP.  Some combinations (possibly lower MERV rating, actually), may produce higher CADR, this remains to be elucidated.  Different brands may also give higher CADR, 3M is generally the best but they are 2.8 times the price of the Dafco ones we are currently using.