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Phylogenetic network analysis of SARS-CoV-2 genomes
Peter Forster1,2,3, Lucy Forster4, Colin Renfrew5
1Institute of Forensic Genetics, 48161 Münster, Germany; pf223@cam.ac.uk acr10@cam.ac.uk.
Summary
Phylogenetic analysis of SARS-CoV-2 genomes identified three main variants (A, B, C). Variants A and C spread globally, while B remained prevalent in East Asia, suggesting geographical resistance or founder effects.
Area of Science:
- Genomics
- Virology
- Epidemiology
Background:
- Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread globally, causing the coronavirus disease 2019 (COVID-19) pandemic.
- Understanding the genetic diversity and transmission patterns of SARS-CoV-2 is crucial for effective public health interventions.
Purpose of the Study:
- To analyze the phylogenetic relationships of SARS-CoV-2 genomes.
- To identify distinct viral variants and their geographical distribution.
- To assess the utility of phylogenetic networks in tracing infection sources.
Main Methods:
- Phylogenetic network analysis was performed on 160 complete human SARS-CoV-2 genomes.
- Comparison with a bat outgroup coronavirus was used to determine the ancestral type.
Main Results:
- Three central SARS-CoV-2 variants (A, B, and C) were identified based on amino acid changes, with A as the ancestral type.
- Variants A and C were found in significant proportions in Europeans and Americans, while variant B was most common in East Asia.
- The spread of the ancestral B type outside East Asia was limited without prior mutation, suggesting potential resistance or founder effects.
Conclusions:
- Phylogenetic networks can effectively trace SARS-CoV-2 transmission routes, including undocumented cases.
- This approach can aid in identifying and quarantining infection sources to prevent further global spread.
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