Gene

Linguistics

Philosophy

Biology

Silent mutation

Nonsynonymous substitution

Missense mutation

Mutation

Viral evolution

Selection (genetic algorithm)

Computer science

Molecular evolution

Lineage (genetic)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Coronavirus disease 2019 (COVID-19)

Evolutionary biology

Genetics

Phylogenetic tree

Divergence (linguistics)

Genome

Recombination

Neutral theory of molecular evolution

Codon usage bias

Infectious disease (medical specialty)

Synonymous substitution

Artificial intelligence

Medicine

Convergent evolution

Most recent common ancestor

Negative selection

Genetic Fitness

Disease

Natural selection

Pathology

Virus Evolution

Human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is most closely related, by average genetic distance, to two coronaviruses isolated from bats, RaTG13 and RmYN02. However, there is a segment of high amino acid similarity between human SARS-CoV-2 and a pangolin-isolated strain, GD410721, in the receptor-binding domain (RBD) of the spike protein, a pattern that can be caused by either recombination or by convergent amino acid evolution driven by natural selection. We perform a detailed analysis of the synonymous divergence, which is less likely to be affected by selection than amino acid divergence, between human SARS-CoV-2 and related strains. We show that the synonymous divergence between the bat-derived viruses and SARS-CoV-2 is larger than between GD410721 and SARS-CoV-2 in the RBD, providing strong additional support for the recombination hypothesis. However, the synonymous divergence between pangolin strain and SARS-CoV-2 is also relatively high, which is not consistent with a recent recombination between them, instead, it suggests a recombination into RaTG13. We also find a 14-fold increase in the

Synonymous mutations and the molecular evolution of SARS-CoV-2 origins