As far as I know, in EnergyPlus (by itself) you'd need some sort of workaround, but there might be an EMS-based approach that I'm not aware of. A couple of options that might work if the simulation you wish to do doesn't couple with the energy simulation in any way are (1) write out all the linkage flows and put together the contaminant simulation yourself or (2) write out all the zone temperatures and use that to schedule a CONTAM model's zone temperature. I've used that second option several times with some success. The downside of scheduling all the zonal temperatures is that it takes some work to get that all connected up correctly and it is easy to make mistakes. CONTAM's cosimulation feature would do this more directly and might require less model-specific work. And it's probably a more general solution.

Jason is correct that co-simulation will provide a more general approach that allows you to directly incorporate filters in airflow paths. I suppose (I have not done this) you could also implement one of the contaminant removal methods offered by EnergyPlus, e.g., deposition velocity or rate. I'm not sure if EnergyPlus tracks the amount of removal, but CONTAM will. Further, CONTAM will enable you to partition the particles into more size bins and associate these bins with different filtration and deposition rates.