Evaluating the Structural and Functional Consequences of SARS-CoV-2 Spike Protein Mutations: A protocol for a Systematic Review and Meta-Analysis of In Silico Studies
Authors: Mushebenge Aganze Gloire-Aime , Ugbaja Samuel Chima , Mbatha Nonkululeko Avril , Riziki Manimani Ghislain , Muzumbukilwa Tambwe Willy , kadima Mukanda Gedeon , Nlooto Manimbulu , Kumalo Hezekiel M. 
Published: August 2023

Abstract
Background
The emergence of new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations in the spike protein has raised concerns regarding their potential implications on the effectiveness of vaccines and therapeutics. In silico studies have emerged as a powerful tool for predicting the impact of mutations on the structure and function of proteins, including the spike protein of SARS-CoV-2. This systematic review and meta-analysis aims to assess the structural and functional consequences of SARS-CoV-2 spike protein mutations through an evaluation of the available in silico studies.
Methods/Design
A comprehensive search of multiple databases including PubMed, Scopus, Web of Science, and Google Scholar will be conducted to identify relevant studies. In silico studies that investigate the structural and functional consequences of SARS-CoV-2 spike protein mutations will be included. The primary outcome of interest will be the effects of mutations on the binding affinity of the spike protein to the angiotensin-converting enzyme 2 (ACE2) receptor, which is essential for virus entry into host cells. The quality of the studies will be assessed using established criteria, and a meta-analysis will be conducted to combine the results of the studies into a single estimate of the effects of the mutations. The analysis of data will be carried out by utilizing two software tools - Review Manager software (version 5.3.5) and R software (version 3.6.1). To determine statistical heterogeneity, a standard chi-square test will be applied with a significance level of P < 0.10. Potential biases related to study size (such as publication bias) will be examined through the application of several techniques, including funnel plots, Egger's test, Begg's test, as well as Trim and Fill analysis.
Results and conclusion
The findings of this systematic review and meta-analysis will provide a comprehensive evaluation of the structural and functional consequences of SARS-CoV-2 spike protein mutations, highlighting the potential implications of these mutations for the development of effective interventions against the virus. The results of the review will contribute to our understanding of the impact of these mutations on the binding affinity of the spike protein to the ACE2 receptor, informing the development of new interventions to combat the virus and its variants. The review will also identify gaps in knowledge and highlight areas for future research, providing a valuable resource for researchers and practitioners in the field of vaccine and drug development.
Ethics and Dissemination: Since the data to be analysed in this study has already been published, there will be no involvement of human subjects and no data will be collected directly from them. Therefore, the study will not require ethical clearance.
Registration Details: This protocol has been registered with the International Prospective Registry of Systematic Reviews (PROSPERO) registration number “CRD42023409682” (https://www.crd.york.ac.uk/prospero/display_record.asp?ID=CRD42023409682).