Phylogenetic network analysis of SARS-CoV-2 genomes

Proc Natl Acad Sci U S A. 2020 Apr 28;117(17):9241-9243. doi: 10.1073/pnas.2004999117. Epub 2020 Apr 8.

Abstract

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.

Keywords: SARS-CoV-2 evolution; ancestral type; subtype.

MeSH terms

  • Animals
  • Betacoronavirus / genetics*
  • COVID-19
  • Chiroptera / virology
  • Coronavirus Infections / virology*
  • Genome, Viral
  • Humans
  • Pandemics
  • Phylogeny
  • Pneumonia, Viral / virology*
  • SARS Virus / genetics
  • SARS-CoV-2