All the fees mentioned in § 58.1-3314 shall be collected by the clerks of the courts of record of the counties and cities at the time of recording the deed or will or upon the confirmation of a commissioner’s report of partition, or at the time an entry is made by the commissioner under § 58.1-3308, which fee shall be paid by the vendee. In the case of lands acquired in fee simple by the Commonwealth, the quantity of land in each case shall be deducted from the land of the prior owner, but shall not be transferred to the Commonwealth, nor shall any transfer or other fee be charged or collected thereon.