Prevalence of COVID-19 genomic variation in Africa: a living systematic review protocol

Objective: The objective of this living systematic review is to synthesize the available evidence on the prevalence of types of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic variations in Africa. Introduction: The burden of the coronavirus disease 2019 (COVID-19) pandemic on the health, well-being, and global economy (especially the fragile economies of African countries) is significant. Profiling the genomic and geographical variations of SARS-CoV-2, a causative agent of COVID-19, may be important for future decision-making, policy guidelines, and development of drugs and vaccines. However, little is known about the up-to-date prevalence of genomic and geographical variations of SARS-CoV-2 virus on the African continent. Inclusion criteria: This living systematic review will include studies on the prevalence of SARS-CoV-2 genetic strains and mutations obtained from sequencing data of samples from individuals of all ages and sexes using the next generation sequencing approaches in studies conducted in Africa. Methods: The search strategy will be developed to retrieve both published and unpublished data. Published data will be obtained from electronic databases. Unpublished data will be obtained from conference proceedings, preprints, theses/dissertations, electronic search engines, and COVID-19-dedicated websites. Relevant published or unpublished data in the English language from January 2020 will be considered. Studies will be selected based on the inclusion criteria of the review. The selected studies will be critically appraised for methodological quality by two independent reviewers and data extracted from eligible studies. Finally, meta-analysis will be done, if feasible, to pool prevalence estimates after heterogeneity of the data has been analyzed. Systematic review registration number: PROSPERO CRD42020211451