Mutation density changes in SARS-CoV-2 are related to the pandemic stage but to a lesser extent in the dominant strain with mutations in spike and RdRp

Doğa EskierYavuz Oktay


Since its emergence in Wuhan, China in late 2019, the origin and evolution of SARS-CoV-2 have been among the most debated issues related to COVID-19. Throughout its spread around the world, the viral genome continued acquiring new mutations and some of them became widespread. Among them, 14408 C>T and 23403 A>G mutations in RdRp and S, respectively, became dominant in Europe and the US, which led to debates regarding their effects on the mutability and transmissibility of the virus. In this study, we aimed to investigate possible differences between time-dependent variation of mutation densities (MDe) of viral strains that carry these two mutations and those that do not. Our analyses at the genome and gene level led to two important findings: First, time-dependent changes in the average MDe of circulating SARS-CoV-2 genomes showed different characteristics before and after the beginning of April, when daily new case numbers started levelling off. Second, this pattern was much delayed or even non-existent for the "mutant" (MT) strain that harbored both 14408 C>T and 23403 A>G mutations. Although these differences were not limited to a few hotspots, it is intriguing that the MDe increase is most evident in two critical genes, S a...Continue Reading

Associated Datasets


Jul 6, 2010·Nucleic Acids Research·Kai WangHakon Hakonarson
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Feb 6, 2020·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Julien Riou, Christian L Althaus
Feb 23, 2020·The Lancet Infectious Diseases·Ensheng DongLauren Gardner
Mar 11, 2020·Cell·Alexandra C WallsDavid Veesler
Mar 30, 2020·Cell·Yong-Zhen Zhang, Edward C Holmes
Apr 15, 2020·Turkish Journal of Medical Sciences·Eskild Petersen, Deniz Gökengin
Apr 24, 2020·Journal of Translational Medicine·Maria PachettiRudy Ippodrino
May 13, 2020·Indian Journal of Medical Ethics·Saurav Basu
May 31, 2020·Influenza and Other Respiratory Viruses·Justin WongLiling Chaw
Jun 9, 2020·BioRxiv : the Preprint Server for Biology·Mary Hongying ChengIvet Bahar
Jun 9, 2020·BioRxiv : the Preprint Server for Biology·Michael WorobeyPhilippe Lemey
Jun 9, 2020·MedRxiv : the Preprint Server for Health Sciences·Ramon Lorenzo-RedondoEgon A Ozer
Jun 27, 2020·BioRxiv : the Preprint Server for Biology·Zharko DaniloskiNeville E Sanjana
Jun 27, 2020·BioRxiv : the Preprint Server for Biology·Lizhou ZhangHyeryun Choe
Jul 9, 2020·BioRxiv : the Preprint Server for Biology·Leonid YurkovetskiyJeremy Luban
Aug 4, 2020·PeerJ·Doğa EskierYavuz Oktay

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