TY - JOUR AU - Martin, Darren P. AU - Lytras, Spyros AU - Lucaci, Alexander G. AU - Maier, Wolfgang AU - Grüning, Björn AU - Shank, Stephen D. AU - Weaver, Steven AU - MacLean, Oscar A. AU - Orton, Richard J. AU - Lemey, Philippe AU - Boni, Maciej F. AU - Tegally, Houriiyah AU - Harkins, Gordon W. AU - Scheepers, Cathrine AU - Bhiman, Jinal N. AU - Everatt, Josie AU - Amoako, Daniel G. AU - San, James Emmanuel AU - Giandhari, Jennifer AU - Sigal, Alex AU - Williamson, Carolyn AU - Hsiao, Nei-yuan AU - von Gottberg, Anne AU - de Klerk, Arné AU - Shafer, Robert W AU - Robertson, David L. AU - Wilkinson, Robert J AU - Sewell, B Trevor AU - Lessells, Richard J. AU - Nekrutenko, Anton AU - Greaney, Allison J AU - Starr, Tyler N AU - Bloom, Jesse D AU - Murrell, Ben AU - Wilkinson, Eduan AU - Gupta, Ravindra K. AU - De Oliveira, Tulio AU - Kosakovsky Pond, Sergei L. PY - 2022 DA - April TI - Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA.1 that likely impact Spike function JO - Molecular Biology and Evolution VL - 39 IS - 4 DO - http://dx.doi.org/10.1093/molbev/msac061 AB - Among the 30 nonsynonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of the S-gene at sites that will likely impact (1) interactions between subunits of the Spike trimer and the predisposition of subunits to shift from down to up configurations, (2) interactions of Spike with ACE2 receptors, and (3) the priming of Spike for membrane fusion. We show here that, based on both the rarity of these 13 mutations in intrapatient sequencing reads and patterns of selection at the codon sites where the mutations occur in SARS-CoV-2 and related sarbecoviruses, prior to the emergence of Omicron the mutations would have been predicted to decrease the fitness of any virus within which they occurred. We further propose that the mutations in each of the three clusters therefore cooperatively interact to both mitigate their individual fitness costs, and, in combination with other mutations, adaptively alter the function of Spike. Given the evident epidemic growth advantages of Omicron overall previously known SARS-CoV-2 lineages, it is crucial to determine both how such complex and highly adaptive mutation constellations were assembled within the Omicron S-gene, and why, despite unprecedented global genomic surveillance efforts, the early stages of this assembly process went completely undetected. PB - Oxford University Press UR - http://eprints.gla.ac.uk/268456/ KW - Coronavirus (COVID-19) ER