RdRp mutations are associated with SARS-CoV-2 genome evolution

Doğa Eskier; Gökhan Karakülah; Aslı Suner; Yavuz Oktay

doi:10.7717/peerj.9587

RdRp mutations are associated with SARS-CoV-2 genome evolution

PeerJ. 2020 Jul 21:8:e9587. doi: 10.7717/peerj.9587. eCollection 2020.

Authors

Doğa Eskier^#^{1

2}, Gökhan Karakülah^#^{1

2}, Aslı Suner³, Yavuz Oktay^{1

2

4}

Affiliations

¹ Izmir Biomedicine and Genome Center (IBG), Izmir, Turkey.
² Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey.
³ Department of Biostatistics and Medical Informatics, Faculty of Medicine, Ege University, Izmir, Turkey.
⁴ Faculty of Medicine, Department of Medical Biology, Dokuz Eylül University, Izmir, Turkey.

^# Contributed equally.

Abstract

COVID-19, caused by the novel SARS-CoV-2 virus, started in China in late 2019, and soon became a global pandemic. With the help of thousands of viral genome sequences that have been accumulating, it has become possible to track the evolution of the viral genome over time as it spread across the world. An important question that still needs to be answered is whether any of the common mutations affect the viral properties, and therefore the disease characteristics. Therefore, we sought to understand the effects of mutations in RNA-dependent RNA polymerase (RdRp), particularly the common 14408C>T mutation, on mutation rate and viral spread. By focusing on mutations in the slowly evolving M or E genes, we aimed to minimize the effects of selective pressure. Our results indicate that 14408C>T mutation increases the mutation rate, while the third-most common RdRp mutation, 15324C>T, has the opposite effect. It is possible that 14408C>T mutation may have contributed to the dominance of its co-mutations in Europe and elsewhere.

Keywords: COVID-19; Mutation rate; RNA-dependent RNA polymerase; RdRp; SARS-CoV-2.

Grants and funding

Yavuz Oktay is supported by the Turkish Academy of Sciences Young Investigator Program (TÜBA-GEBİP). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.