The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Martin, D. P, Weaver, S., Tegally, H., San, J. E., Shank, S. D, Wilkinson, E., Lucaci, A. G, Giandhari, J., Naidoo, S., Pillay, Y., Singh, L., Lessells, R. J, Gupta, R. K, Wertheim, J. O, Nekturenko, A., Murrell, B., Harkins, G. W, Lemey, P., MacLean, O. A, Robertson, D. L, de Oliveira, T., & Pond, S. L K. Cell, 184(20):5189–5200, Elsevier, sep, 2021.

Paper doi abstract bibtex

Summary The independent emergence late in 2020 of the B.1.1.7, B.1.351, and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to overcome public health interventions and rising population immunity. Here, by examining patterns of synonymous and non-synonymous mutations that have accumulated in SARS-CoV-2 genomes since the pandemic began, we find that the emergence of these three "501Y lineages" coincided with a major global shift in the selective forces acting on various SARS-CoV-2 genes. Following their emergence, the adaptive evolution of 501Y lineage viruses has involved repeated selectively favored convergent mutations at 35 genome sites, mutations we refer to as the 501Y meta-signature. The ongoing convergence of viruses in many other lineages on this meta-signature suggests that it includes multiple mutation combinations capable of promoting the persistence of diverse SARS-CoV-2 lineages in the face of mounting host immune recognition.

@article{Martin2021a,
abstract = {Summary The independent emergence late in 2020 of the B.1.1.7, B.1.351, and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to overcome public health interventions and rising population immunity. Here, by examining patterns of synonymous and non-synonymous mutations that have accumulated in SARS-CoV-2 genomes since the pandemic began, we find that the emergence of these three "501Y lineages" coincided with a major global shift in the selective forces acting on various SARS-CoV-2 genes. Following their emergence, the adaptive evolution of 501Y lineage viruses has involved repeated selectively favored convergent mutations at 35 genome sites, mutations we refer to as the 501Y meta-signature. The ongoing convergence of viruses in many other lineages on this meta-signature suggests that it includes multiple mutation combinations capable of promoting the persistence of diverse SARS-CoV-2 lineages in the face of mounting host immune recognition.},
author = {Martin, Darren P and Weaver, Steven and Tegally, Houriiyah and San, James Emmanuel and Shank, Stephen D and Wilkinson, Eduan and Lucaci, Alexander G and Giandhari, Jennifer and Naidoo, Sureshnee and Pillay, Yeshnee and Singh, Lavanya and Lessells, Richard J and Gupta, Ravindra K and Wertheim, Joel O and Nekturenko, Anton and Murrell, Ben and Harkins, Gordon W and Lemey, Philippe and MacLean, Oscar A and Robertson, David L and de Oliveira, Tulio and Pond, Sergei L Kosakovsky},
doi = {10.1016/J.CELL.2021.09.003},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Martin et al. - 2021 - The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.pdf:pdf},
issn = {0092-8674},
journal = {Cell},
keywords = {COVID 19,convergent mutations,directional selection,diversifying selection,evolutionary adaptation,genomics{\_}fund{\_}ack,immune evasion,lineage-defining mutations,original,positive selection,recurrent mutations,transmission advantage},
mendeley-tags = {genomics{\_}fund{\_}ack,original},
month = {sep},
number = {20},
pages = {5189--5200},
pmid = {34537136},
publisher = {Elsevier},
title = {{The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages}},
url = {http://www.cell.com/article/S0092867421010503/fulltext http://www.cell.com/article/S0092867421010503/abstract https://www.cell.com/cell/abstract/S0092-8674(21)01050-3},
volume = {184},
year = {2021}
}

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