Phylogenetic network analysis of SARS-CoV-2 genomes

By P. Forster, Lucy Forster, C. Renfrew, M. Forster. Proceedings of the National Academy of Sciences of the United States of America, 2020

969 citations recorded by the source corpus.

Significance This is a phylogenetic network of SARS-CoV-2 genomes sampled from across the world. These genomes are closely related and under evolutionary selection in their human hosts, sometimes with parallel evolution events, that is, the same virus mutation emerges in two different human hosts. This makes character-based phylogenetic networks the method of choice for reconstructing their evolutionary paths and their ancestral genome in the human host. The network method has been used in around 10,000 phylogenetic studies of diverse organisms, and is mostly known for reconstructing the prehistoric population movements of humans and for ecological studies, but is less commonly employed in the field of virology. In a phylogenetic network analysis of 160 complete human severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) genomes, we find three central variants distinguished by amino acid changes, which we have named A, B, and C, with A being the ancestral type according to the bat outgroup coronavirus. The A and C types are found in significant proportions outside East Asia, that is, in Europeans and Americans. In contrast, the B type is the most common type in East Asia, and its ancestral genome appears not to have spread outside East Asia without first mutating into derived B types, pointing to founder effects or immunological or environmental resistance against this type outside Asia. The network faithfully traces routes of infections for documented coronavirus disease 2019 (COVID-19) cases, indicating that phylogenetic networks can likewise be successfully used to help trace undocumented COVID-19 infection sources, which can then be quarantined to prevent recurrent spread of the disease worldwide.

Subfields: Genetics, Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3212a6420fe579fc6f036bac29e7551484e1b126

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

1. B. Hu
2. Shaoying Huang
3. L. Yin

Citations in the corpus

• COVID-19: The first documented coronavirus pandemic in history (2020, neutral): “Nevertheless, a recent study claimed that three genetic types of the virus have been circulating globally [37].”
• The cytokine storm and COVID‐19 (2020, background): “It has been found that SARS‐CoV‐2 genomes from different parts of the world have evolved in different clusters.(22,23) Forster et al(23) reported there to be at least three central variants of SARS‐CoV‐2 globally, named A, B, and C.”