Shabir has co-authored over 650 scientific publications since 1997, and has an H-index of 103. His research has focused on the epidemiology, and clinical development of lifesaving vaccines against pneumonia and diarrheal disease. Over the past decade, he has focussed on vaccines being developed for immunization of pregnant women for the benefit of the women and their young infants. He led the first two COVID-19 vaccine studies undertaken in Africa, and was also involved in multiple clinical and serology epidemiology studies on COVID-19.