Advancing FAIR phylogenetics for health threats: a systematic review of SARS-CoV-2 research and guidelines for future outbreaks.

During the COVID-19 pandemic, the need for quick public health action often conflicted with the careful methods required in phylogenetics. To explore this, we reviewed 217 SARS-CoV-2 studies published from January 2020 to March 2025 in 121 journals. We found many methodological problems that weaken the reliability and reproducibility of these studies. Key issues include missing outgroup sampling, which affects ingroup topology, tree rooting and how we interpret evolutionary changes and relationships. Another issue is the lack of gene annotations, which can cause characters from one gene to align with those of a different gene. Many studies also misinterpret support or other branch statistics, treating them as proof of clade accuracy instead of as measures of relative evidence. In addition, 91% of the studies do not follow FAIR (Findable, Accessible, Interoperable, and Reusable) data principles, with data and code often unavailable. Finally, we also found a "prestige paradox": journals with higher impact factors do not necessarily have better methods or transparency. Therefore, we offer simple guidelines for authors, reviewers and editors to improve transparency and FAIR data standards in viral phylogenetics, making writing and reviewing papers easier, ensuring published phylogenetic analyses remain a trustworthy resource for future pandemics.