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. 2020 Apr 28;117(17):9241-9243.
doi: 10.1073/pnas.2004999117. Epub 2020 Apr 8.

Phylogenetic network analysis of SARS-CoV-2 genomes

Peter Forster  1   2   3 , Lucy Forster  4 , Colin Renfrew  5 , Michael Forster  3   6
Affiliations

Phylogenetic network analysis of SARS-CoV-2 genomes

Peter Forster et al. Proc Natl Acad Sci U S A. .

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.

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Conflict of interest statement

The authors declare no competing interest.

Figures

Fig. 1.
Fig. 1.
Phylogenetic network of 160 SARS-CoV-2 genomes. Node A is the root cluster obtained with the bat (R. affinis) coronavirus isolate BatCoVRaTG13 from Yunnan Province. Circle areas are proportional to the number of taxa, and each notch on the links represents a mutated nucleotide position. The sequence range under consideration is 56 to 29,797, with nucleotide position (np) numbering according to the Wuhan 1 reference sequence (8). The median-joining network algorithm (2) and the Steiner algorithm (9) were used, both implemented in the software package Network5011CS (https://www.fluxus-engineering.com/), with the parameter epsilon set to zero, generating this network containing 288 most-parsimonious trees of length 229 mutations. The reticulations are mainly caused by recurrent mutations at np11083. The 161 taxa (160 human viruses and one bat virus) yield 101 distinct genomic sequences. The phylogenetic diagram is available for detailed scrutiny in A0 poster format (SI Appendix, Fig. S5) and in the free Network download files.
See this image and copyright information in PMC

Comment in

  • Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary.
    Sánchez-Pacheco SJ, Kong S, Pulido-Santacruz P, Murphy RW, Kubatko L. Sánchez-Pacheco SJ, et al. Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12518-12519. doi: 10.1073/pnas.2007062117. Epub 2020 May 7. Proc Natl Acad Sci U S A. 2020. PMID: 32381733 Free PMC article. No abstract available.
  • Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
    Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M. Mavian C, et al. Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12522-12523. doi: 10.1073/pnas.2007295117. Epub 2020 May 7. Proc Natl Acad Sci U S A. 2020. PMID: 32381734 Free PMC article. No abstract available.
  • Evolving COVID-19 conundrum and its impact.
    Chookajorn T. Chookajorn T. Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12520-12521. doi: 10.1073/pnas.2007076117. Epub 2020 May 7. Proc Natl Acad Sci U S A. 2020. PMID: 32381737 Free PMC article. No abstract available.

References

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