On the origin and evolution of SARS-CoV-2

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the ongoing global outbreak of a coronavirus disease (herein referred to as COVID-19). Other viruses in the same phylogenetic group have been responsible for previous regional outbreaks, including SARS and MERS. SARS-CoV-2 has a zoonotic origin, similar to the causative viruses of these previous outbreaks. The repetitive introduction of animal viruses into human populations resulting in disease outbreaks suggests that similar future epidemics are inevitable. Therefore, understanding the molecular origin and ongoing evolution of SARS-CoV-2 will provide critical insights for preparing for and preventing future outbreaks. A key feature of SARS-CoV-2 is its propensity for genetic recombination across host species boundaries. Consequently, the genome of SARS-CoV-2 harbors signatures of multiple recombination events, likely encompassing multiple species and broad geographic regions. Other regions of the SARS-CoV-2 genome show the impact of purifying selection. The spike (S) protein of SARS-CoV-2, which enables the virus to enter host cells, exhibits signatures of both purifying selection and ancestral recombination events, leading to an effective S protein capable of infecting human and many other mammalian cells. The global spread and explosive growth of the SARS-CoV-2 population (within human hosts) has contributed additional mutational variability into this genome, increasing opportunities for future recombination.
COVID-19: How genome evolution helped spur a global pandemic A confluence of historic gene swapping and evolutionary optimizations and adaptations helped make the coronavirus causing COVID-19 so infectious to people. Devika Singh and Soojin Yi from the Georgia Institute of Technology in Atlanta, USA, discuss the molecular evidence for ancestral recombination events and natural selection in the genome of SARS-CoV-2, the coronavirus responsible for COVID-19. In particular, the spike protein that enables viral entry into human cells shows ample signs of these evolutionary processes, which probably facilitated the virus’s spillover from other animals into humans. New variants of SARS-CoV-2 that have rapidly spread during the pandemic point to ongoing evolutionary processes, including effects of both potential functional alteration and random genetic drift. A better understanding of the virus’s evolutionary trajectory could help inform efforts to contain SARS-CoV-2 and prevent future pandemics.