Named parameters are not supported by JPA in native queries, only for JPQL. You must use positional parameters.

Named parameters follow the rules for identifiers defined in Section 4.4.1. The use of named parameters applies to the Java Persistence query language, and is not defined for native queries. Only positional parameter binding may be portably used for native queries.

So, use this

Query q = em.createNativeQuery("SELECT count(*) FROM mytable where username = ?1");
q.setParameter(1, "test");

While JPA specification doesn’t support named parameters in native queries, some JPA implementations (like Hibernate) may support it

Native SQL queries support positional as well as named parameters

However, this couples your application to specific JPA implementation, and thus makes it unportable.