PHYLOGENETIC NETWORKS IN THE STUDY OF SARS-COV-2

PANDEMICS & EVOLUTION

Ignatius Danny Pattirajawane1

Abstract

Unlike the influenza pandemic in the early twentieth century, scientists have identified the viral
agents responsible for current SARS-CoV-2 pandemic. Moreover, scientists also have provided
complete genome sequences of the virus shortly after the breakout in Wuhan, China in December
2019. Those achievement has been made possible not only because of the development of
sequencing technology but also of the contribution of mathematics and computational biology in
the field of bioinformatics. In the study of evolution phylogenetic tree approach give major
drawback when reticulations such as lateral gene transfers, hybridization and recombination
happened. And phylogenetic tree method could produce collection of trees because of
incompatible phylogenetic signals. Thus, instead of the commonly used phylogenetic tree, one of
the approaches in phylogenetic analysis in bioinformatics when the reticulations and incompatible
signals were addressed is phylogenetic networks. In this article, we give literatures review of the
commonly used phylogenetic network method and literature review of the use of phylogenetics
networks method in the study of current SARS-CoV-2 pandemics and its evolution. We also
provided phylogenetics networks analysis of 9 complete genome sequences consist of 3 SARS-
CoV-2 isolates from human, 1 from bat, 4 pangolin hosts, and 1 coronavirus isolate from human
host. The genome sequences were acquired from GenBank-NCBI database and similarity plot of
the sequences were analysed to detect recombination events. Phylogenetic networks were drawn
by using Neighbor-Net and Median Networks algorithm.

Keywords: phylogenetic networks, recombination, reticulation, SARS-CoV-2