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Microbes & Immunity SARS-CoV-2 complementary classification

present mutation rates, unforeseen selective pressures may Acknowledgments
alter these trajectories. Second, although SARS-CoV-2 has
exhibited limited divergence to date, the potential for future None.
recombination or adaptive mutations remains. Third, while Funding
the analysis included the most epidemiologically significant
SARS-CoV-2 variants, it may not capture the evolutionary None.
dynamics of rare or geographically restricted lineages. Conflict of interest
Fourth, evolutionary rate estimates are constrained by the
availability and geographic distribution of sequencing data, The authors declare they have no competing interests.
which may overrepresent certain SARS-CoV-2 variants
due to sequencing concentration in high-income countries. Author contributions
Fifth, although recombination was incorporated into the Conceptualization: Malik Sallam
modeling, its true long-term impact on divergence is not Data curation: All authors
fully understood. Sixth, inferences about transmissibility Formal analysis: Saja Al-Baidhani, Malik Sallam
were drawn from epidemiological data rather than direct Investigation: All authors
experimental comparisons, which were beyond the scope of Methodology: All authors
this study. Finally, while the proposed classification system Project administration: Malik Sallam
aims to guide future policy and research, its global adoption Supervision: Malik Sallam
will require coordination and consensus among international Validation: Saja Al-Baidhani, Malik Sallam
public health authorities with potentially divergent priorities. Visualization: Malik Sallam
Writing – original draft: Malik Sallam
5. Conclusion Writing – review & editing: All authors
The classification of SARS-CoV-2 variants has profoundly
shaped public health policy, vaccine development, and Ethics approval and consent to participate
global perceptions throughout the pandemic. However, the Not applicable.
analysis suggests that many of these classifications have not
been consistently anchored in robust virological criteria, Consent for publication
highlighting an opportunity to enhance the present system Not applicable.
with more biologically grounded standards. Comparative
genomic analyses demonstrate that the maximum Availability of data
divergence among SARS-CoV-2 variants (0.006 s/s) is
substantially below the thresholds used to define subtypes The data presented in this study are available on request
in HIV-1, HCV, or influenza A virus. Even under accelerated from the corresponding author (Malik Sallam).
evolutionary scenarios, the virus would require centuries References
to reach divergence levels warranting lineage designation.
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unpredictable viral evolution and instead suggest that acute respiratory syndrome-related coronavirus: Classifying
SARS-CoV-2 remains evolutionarily constrained. The 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol.
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to public confusion, reactionary policy decisions, and the doi: 10.1038/s41564-020-0695-z
diversion of scientific resources. To address these issues, an 2. Lu R, Zhao X, Li J, et al. Genomic characterisation and
evidence-based framework integrating genetic, functional, epidemiology of 2019 novel coronavirus: Implications
and epidemiological criteria is proposed to classify SARS- for virus origins and receptor binding. Lancet.
CoV-2 variants. Under this proposed framework, none 2020;395(10224):565-574.
of the existing SARS-CoV-2 VOCs meet the combined doi: 10.1016/s0140-6736(20)30251-8
genetic and functional thresholds typically required for
lineage-level classification in other RNA viruses. Rather 3. Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak
associated with a new coronavirus of probable bat origin.
than replacing present classification systems, the proposed Nature. 2020;579(7798):270-273.
approach advocates for a paradigm shift that distinguishes
persistent evolutionary patterns from short-term genetic doi: 10.1038/s41586-020-2012-7
fluctuations – to support more proportionate, evidence- 4. Rosen CJ. Viral variants, vaccinations, and long covid - new
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Volume 2 Issue 3 (2025) 100 doi: 10.36922/MI025190042