To minimize the indoor transmission of contaminants, such as the virus that can lead to COVID-19, buildings must provide the best indoor air quality possible. Improving indoor air quality can be achieved through the building's HVAC system to decrease any concentration of indoor contaminants by dilution and/or by source removal. However, doing so has practical downsides on the HVAC operation that are not always quantified in the literature. This paper develops a temporal simulation capability that is used to investigate the indoor virus concentration and operational cost of an HVAC system for two mitigation strategies: (1) supplying 100% outdoor air into the building and (2) using different HVAC filters, including MERV 10, MERV 13, and HEPA filters. These strategies are applied to a hypothetical medium office building consisting of five occupied zones and located in a cold and dry climate. We modeled the building using the Modelica Buildings library and developed new models for HVAC filtration and virus transmission to evaluate COVID-19 scenarios. We show that the ASHRAE-recommended MERV 13 filtration reduces the average virus concentration by about 10% when compared to MERV 10 filtration, with an increase in site energy consumption of about 3%. In contrast, the use of 100% outdoor air reduces the average indoor concentration by about an additional 1% compared to MERV 13 filtration, but significantly increases heating energy consumption. Use of HEPA filtration increases the average indoor concentration and energy consumption compared to MERV 13 filtration due to the high resistance of the HEPA filter.