Advancing FAIR Phylogenetics for Health Threats: A Systematic Review of SARS-CoV-2 Research and Guidelines for Future Outbreaks

Supplementary Materials

Manuscript Title

"Advancing FAIR Phylogenetics for Health Threats: A Systematic Review of SARS-CoV-2 Research and Guidelines for Future Outbreaks."

Authors

Omkar Marne (1,2)

Denis Jacob Machado (1,2)

Affiliation

University of North Carolina at Charlotte (UNC Charlotte), College of Computing and Informatics (CCI), Department of Bioinformatics and Genomics, Charlotte, NC, USA.

University of North Carolina at Charlotte (UNC Charlotte), Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Charlotte, NC, USA.

Overview

This repository contains all figures, datasets, and supporting materials associated with the systematic review of 217 phylogenetic studies of SARS-CoV-2. The materials are organized to ensure transparency, reproducibility, and compliance with FAIR data principles.

Figures

Figure 1: Workflow of Phylogenetic Analysis

File: figure_1.pdf

Description: The workflow of a phylogenetic analysis. White boxes indicate the primary operational stages, while the connected grey boxes highlight a selected subset of the methodological choices required at each step. These lists are illustrative rather than exhaustive, demonstrating the complexity of decision-making involved in observation, encoding, tree search, and result interpretation.

Figure 2: PRISMA Flow Diagram

File: figure_2.pdf

Description: The PRISMA flow diagram of the paper selection process used in the present study.

Figure 3: Methodological Patterns Across 217 SARS-CoV-2 Phylogenetic Studies

File: figure_3.pdf

Description: Overview of methodological patterns in 217 phylogenetic studies of SARS-CoV-2. (a) Usage of outgroup; (b) Justification of root; (c) Branch statistics; (d) Usage of gene annotation; (e) Compliance with FAIR guidelines; (f) Venn diagram of data type usage; (g) Types of genomic datasets; (h) Optimality criteria and inference strategies. Abbreviations: BI-Bayesian Inference; BS-Bootstrap; CGR-Chaos Game Representation; FAIR-Findable, Accessible, Interoperable, and Reusable; GB-Goodman-Bremer; ML-Maximum Likelihood; NJ-Neighbor-Joining; P-Parsimony; PP-Posterior Probabilities; UPGMA-Unweighted Pair Group Method with Arithmetic Mean.

Figure 4: Journal Impact Factor Distribution

File: figure_4.pdf

Description: Temporal and methodological characterization of phylogenetic studies of SARS-CoV-2. (a) Number of papers published per year across the study period. (b) Percentage of papers adhering to each of several quality indicators. Paired bars in (b) contrast studies published before 2023 (white) with those published in 2023 or later (gray). Error bars represent 95% Wilson score confidence intervals. Annotations above each pair report p and q values (p/q) from two-sided Fisher's exact tests applied per indicator, with Benjamini–Hochberg FDR correction.

Figure 5: Yearly distribution of SARS-CoV-2 phylogenetic studies

File: figure_5.pdf

Description: Distribution of the phylogenetic studies of SARS-CoV-2 based on (a) studies published by year from 2020 to 2025 and (b) reporting quality indicators. Reporting quality indicators are compared between studies published before 2023 (n = 135) and after 2023 (n = 82). The proportion of studies reporting each indicator is shown with 95% Wilson confidence intervals.

Datasets

File review_papers.xlsx

This Excel file contains the complete dataset and metadata extracted from the 217 phylogenetic studies.

File review_papers.csv

This file contains the same dataset as the Excel file, provided in Comma-Separated Values (CSV) format.

File review_papers_APA_format.txt

This file contains the full bibliographic list of the 217 included studies formatted according to APA guidelines.

File checklist.csv

Reporting checklist for phylogenetic analyses of viral pathogens, distributing responsibility across authors, reviewers, and editors. Authors report each item in the indicated section of the manuscript; reviewers verify the item using the cue provided; editors require the item as a submission or acceptance condition. Item F covers FAIR deposition and operates at a different scope than items 1-8.

Statistical Analysis

Please see the compressed zip file stats.zip, and the details on the README_STATS.md file inside of it.

Reproducibility and Transparency Statement

All data were manually curated from peer-reviewed publications. The dataset is provided in open formats (XLSX and CSV) to facilitate reproducibility and reuse.