A variant-dependent molecular clock with anomalous diffusion models SARS-CoV-2 evolution in humans

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans has been monitored at an unprecedented level due to the public health crisis, yet the stochastic dynamics underlying such a process is dubious. Here, considering the number of acquired mutations as the displaceme...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 120; no. 30; p. e2303578120
Main Authors Goiriz, Lucas, Ruiz, Raúl, Garibo-I-Orts, Òscar, Conejero, J Alberto, Rodrigo, Guillermo
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 25.07.2023
SeriesBrief Report
Subjects
Biological Sciences
Coronaviruses
Diffusion rate
Evolution
Gene sequencing
Genomes
Mathematical models
Pandemics
Public health
Severe acute respiratory syndrome coronavirus 2
Stochastic processes
Stochasticity
Time dependence
Viral diseases
whole genome sequencing
stochastic process
anomalous diffusion
dynamic systems
virus evolution rate
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Summary:The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans has been monitored at an unprecedented level due to the public health crisis, yet the stochastic dynamics underlying such a process is dubious. Here, considering the number of acquired mutations as the displacement of the viral particle from the origin, we performed biostatistical analyses from numerous whole genome sequences on the basis of a time-dependent probabilistic mathematical model. We showed that a model with a constant variant-dependent evolution rate and nonlinear mutational variance with time (i.e., anomalous diffusion) explained the SARS-CoV-2 evolutionary motion in humans during the first 120 wk of the pandemic in the United Kingdom. In particular, we found subdiffusion patterns for the Primal, Alpha, and Omicron variants but a weak superdiffusion pattern for the Delta variant. Our findings indicate that non-Brownian evolutionary motions occur in nature, thereby providing insight for viral phylodynamics.
Bibliography:ObjectType-Article-1
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Edited by Eugene Koonin, NIH, Bethesda, MD; received March 20, 2023; accepted June 11, 2023
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.2303578120