Phylogenetics analysis of SARS-CoV-2 spike glycoproteins

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Phylogenetic Tree of Covid Corona Virus with other Species

A novel coronavirus (CoV), named Severe Acute Respiratory Syndrome-CoV-2 (SARS-CoV-2) or nCoV-2019, has emerged since December 2019 from Wuhan city of Hubei province in China [1]. This virus belongs to the coronavirus family from which previous outbreaks have emerged (SARS and MERS). They have been a great threat to public health causing many deaths including  SARS-CoV-2. There is no proper treatment available to cure this coronavirus disease (covid19). Scientists and researchers are trying really hard to develop a drug or a vaccine or a proper way to cure covid19.

In this essence, Bioinformatics Review has built up a team of worldwide researchers to work on covid19. We will be updating all findings we get during this project. The first study we conducted on SARS-CoV-2 is explained as follows.

Phylogenetics analysis of SARS-CoV-2

The phylogenetic tree is shown below. This tree was created using the IQTREE tool [2] and the best model was found using ModelFinder [3].

Fig. 1 Phylogenetic tree of SARS-CoV-2 spike sequences with SARS-CoV spike sequences as an outgroup. The red color denotes SARS-CoV-2 spike sequences and green color denotes SARS-CoV spike sequences. The best model was VT+F4 as selected by the ModelFinder and the tree was constructed with 1000 replications.

The branch lengths of spike sequences suggest the divergence of SARS-CoV from SARS-CoV-2. The multiple sequence alignment (MSA) (Fig. 2) of these sequences shows several conserved regions across the entire alignment (File 1).

Further, experiments are being performed for a complete phylogeny and evolutionary study of these sequences. For all updates regarding Covid19 work being done by our research group, visit this page.



  1. Zhu, N., Zhang, D., & Wang, W. China Novel Coronavirus Investigating and Research Team. A novel coronavirus from patients with pneumonia in China, 2019 [published January 24, 2020]. N Engl J Med.
  2. Nguyen, L. T., Schmidt, H. A., Von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular biology and evolution32(1), 268-274.
  3. Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K., von Haeseler, A., & Jermiin, L. S. (2017). ModelFinder: fast model selection for accurate phylogenetic estimates. Nature methods14(6), 587.
Muniba is a Bioinformatician based in the South China University of Technology. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba
Tariq is founder of Bioinformatics Review and a professional Software Developer at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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