Gene

Marketing

Coronavirus

2019-20 coronavirus outbreak

Biology

Adaptive evolution

Virology

Viral evolution

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Outbreak

Computational biology

Business

Diversification (marketing strategy)

Coronavirus disease 2019 (COVID-19)

Evolutionary biology

Genetics

Genome

Vaccination

Infectious disease (medical specialty)

Medicine

Virus

Pandemic

Disease

Positive selection

Pathology

Proceedings of the National Academy of Sciences

Significance Understanding the ongoing evolution of SARS-CoV-2 is essential to control and ultimately end the pandemic. We analyzed more than 300,000 SARS-CoV-2 genomes available as of January 2021 and demonstrate adaptive evolution of the virus that affects, primarily, multiple sites in the spike and nucleocapsid protein. Selection appears to act on combinations of mutations in these and other SARS-CoV-2 genes. Evolution of the virus is accompanied by ongoing adaptive diversification within and between geographic regions. This diversification could substantially prolong the pandemic and the vaccination campaign, in which variant-specific vaccines are likely to be required.

Ongoing global and regional adaptive evolution of SARS-CoV-2