Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function

Alejandro BerrioG. A. Wray


The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. Such tests cannot, however, detect changes in the function of RNA molecules. Here we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code. We recapitulate the finding that the gene encoding Spike protein has been a target of both purifying and positive selection. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. Homology-directed modeling indicates no change in either Nsp4 or Nsp16 protein struc...Continue Reading


Feb 13, 2001·Virology·T M Gallagher, M J Buchmeier
Jun 25, 2004·Nucleic Acids Research·Yuzhen Ye, Adam Godzik
Jul 9, 2004·Genetics·Wendy S W Wong, Rasmus Nielsen
Oct 29, 2004·Bioinformatics·Sergei L Kosakovsky PondSpencer V Muse
Jul 19, 2005·Genome Research·Adam SiepelDavid Haussler
Aug 9, 2006·Proceedings of the National Academy of Sciences of the United States of America·Wei LuBing Sun
Apr 22, 2008·Nucleic Acids Research·Andreas R GruberIvo L Hofacker
Jan 7, 2009·Cell Research·Tetsuo TsuchidaShizuo Akira
Mar 27, 2009·Proceedings of the National Academy of Sciences of the United States of America·Sandrine BelouzardGary R Whittaker
Apr 28, 2010·PLoS Pathogens·Mickaël BouvetEtienne Decroly
Feb 1, 2011·Briefings in Bioinformatics·Melissa J HubiszAdam Siepel
Feb 25, 2011·Journal of Virology·Marne C HagemeijerCornelis A M de Haan
Oct 14, 2011·Viruses·Leopoldo G GebhardAndrea V Gamarnik
Nov 26, 2011·Algorithms for Molecular Biology : AMB·Ronny LorenzIvo L Hofacker
Mar 8, 2012·Growth Factors·Serge Y Fuchs
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Jun 15, 2014·Virology·Marne C HagemeijerCornelis A M de Haan
Oct 4, 2014·Virus Research·Vineet D MenacheryRalph S Baric
Feb 28, 2015·Methods in Molecular Biology·Anthony R Fehr, Stanley Perlman
May 8, 2015·Nature Protocols·Lawrence A KelleyMichael J E Sternberg
Mar 1, 2016·Molecular Cell·Nathan PirakitikulrAnna M Pyle
Oct 8, 2016·Advances in Virus Research·R MadhugiriJ Ziebuhr
Oct 8, 2016·Advances in Virus Research·R J G HulswitB-J Bosch
Oct 8, 2016·Advances in Virus Research·E J SnijderJ Ziebuhr
Jan 11, 2018·Nature Communications·Andrea MacFaddenJeffrey S Kieft
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