The results demonstrated that the proposed 95% threshold could be used to accurately identify EV types from the top 100 hit sequences in most of the tested prototypes, such as PVs and the major pathogens of HFMD (EV-A71, CVA2, CVA4, CVA10, and CVA16), meningitis (CVA9, CVB2, CVB4, CVB5, and E6, E9, E13, E18, and E30), and AFP (EV-D68). This evidence concerns the gene AFP and meningitis.