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Updated: Dec 13, 2025
07:15
Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
Published on: January 16, 2019
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Variant analysis of SARS-CoV-2 genomes
Takahiko Koyama1, Daniel Platt1, Laxmi Parida1
1IBM TJ Watson Research Center, 1101 Kitchawan Rd, Yorktown Heights, New York 10598, United States of America.
Bulletin of the World Health Organization
|August 4, 2020
Summary
Analysis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genomes revealed numerous variants, with the D614G clade emerging as the most prevalent. Evolutionary analysis suggests structured transmission patterns and potential multiple introductions of the virus into populations.
Area of Science:
- Virology
- Genomics
- Epidemiology
Background:
- Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) exhibits genetic variability.
- Understanding genome variants is crucial for tracking viral evolution and transmission.
Purpose of the Study:
- To analyze the genome variants of SARS-CoV-2.
- To identify common variants and clades within the viral population.
Main Methods:
- Downloaded and analyzed 10,022 SARS-CoV-2 genomes from global databases (February-May 2020).
- Identified nucleotide variants via pairwise alignment to the reference genome.
- Converted coding region variants to amino acid changes.
- Utilized Bayesian evolutionary analysis for clade identification.
Main Results:
- Identified 5,775 distinct genome variants, including missense, synonymous, and non-coding mutations.
- The most common variants were synonymous 3037C>T, P4715L (ORF1ab), and D614G (spike protein).
- Six major clades and 14 subclades were identified, with D614G becoming dominant.
Conclusions:
- Multiple SARS-CoV-2 genome variants exist.
- The D614G clade has become the most common variant since December 2019.
- Evolutionary analysis suggests structured transmission and potential multiple introductions.
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