Aina Muceniece career began at the August Kirhenstein Institute of Biology and later went on to study enteroviruses.
Muceniece's scientific career began at the August Kirhenstein Institute of Microbiology, Latvian Academy of Sciences (Latvian: LZA Augusta Kirhensteina Mikrobiologijas instituts), first as a senior laboratory assistant, later as a senior research associate. Muceniece's laboratory started to study enteroviruses in the 1960s, and the research led to the identification of an echovirus that had possible use to treat melanoma, which became RIGVIR. 
