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Updated: Oct 27, 2025

Live Imaging and Quantification of Viral Infection in K18 hACE2 Transgenic Mice Using Reporter-Expressing Recombinant SARS-CoV-2
Published on: November 5, 2021
Ongoing global and regional adaptive evolution of SARS-CoV-2
Nash D Rochman1, Yuri I Wolf2, Guilhem Faure3
1National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894; nash.rochman@nih.gov zhang@broadinstitute.org Koonin@ncbi.nlm.nih.gov.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution is mainly driven by purifying selection, with key mutations in spike and nucleocapsid proteins indicating positive selection and global diversification shifts during the COVID-19 pandemic.
Area of Science:
- Virology
- Genomics
- Evolutionary Biology
Background:
- Understanding SARS-CoV-2 evolution is critical for controlling the COVID-19 pandemic.
- Over 300,000 SARS-CoV-2 genome sequences from January 2021 were analyzed.
Purpose of the Study:
- To analyze trends in SARS-CoV-2 evolution and identify key genetic changes.
- To understand the impact of mutations on viral diversification and global spread.
Main Methods:
- Phylogenetic analysis of over 300,000 SARS-CoV-2 genome sequences.
- Identification of sites under positive and purifying selection.
- Analysis of viral diversity and geographic partitioning over time.
Main Results:
- SARS-CoV-2 evolution is primarily under purifying selection, with positive selection at specific sites.
- Positively selected sites are enriched in the spike receptor-binding domain and nucleocapsid protein's nuclear localization signals (NLS).
- Four distinct periods of viral evolution were identified, marked by diversification, homogenization (D614G spread), NLS variant prominence, and antibody-evading mutations.
Conclusions:
- Specific mutations in SARS-CoV-2, particularly in the spike and nucleocapsid proteins, drive viral evolution and diversification.
- The emergence of antibody-evading mutations signals potential viral speciation and ongoing pandemic challenges.
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