Update: Selection analysis on spike glycoprotein of SARS-CoV-2

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Figure 1. Protein Structure of Corona Virus - Ribbon View

We have recently conducted a selection pressure analysis on SARS-CoV-2 spike glycoprotein sequences. The analysis revealed not even a single site showing evidence of purifying selection but episodic diversifying selection on three sites. Out of these three sites, two sites are potentially relevant (Fig. 3).

Fig. 3 Structure of Spike Glycoprotein (PDB ID: 6VXX) of SARS-CoV-2. The detected residues under positive selection are shown in red color.

The analysis was performed using Hyphy [1] on the Datamonkey server [2]. BUSTED [3], MEME [4], and FUBAR [5] methods were used. MEME [4] and FUBAR [5] found 3 and 5 sites respectively under positive selection. However, BUSTED [3] did not found any evidence of selection on the tested branches of the phylogeny.

These spike glycoproteins are being analyzed further. Additionally, we are analyzing spike glycoproteins of SARS-CoV for comparison between SARS-CoV and SARS-CoV-2 spike glycoproteins.


  1. Pond, S. L. K., & Muse, S. V. (2005). HyPhy: hypothesis testing using phylogenies. In Statistical methods in molecular evolution (pp. 125-181). Springer, New York, NY.
  2. Weaver, S., Shank, S. D., Spielman, S. J., Li, M., Muse, S. V., & Kosakovsky Pond, S. L. (2018). Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes. Molecular biology and evolution35(3), 773-777.
  3. Murrell, B., Weaver, S., Smith, M. D., Wertheim, J. O., Murrell, S., Aylward, A., … & Scheffler, K. (2015). Gene-wide identification of episodic selection. Molecular biology and evolution32(5), 1365-1371.
  4. Murrell, B., Wertheim, J. O., Moola, S., Weighill, T., Scheffler, K., & Pond, S. L. K. (2012). Detecting individual sites subject to episodic diversifying selection. PLoS genetics8(7).
  5. Murrell, B., Moola, S., Mabona, A., Weighill, T., Sheward, D., Kosakovsky Pond, S. L., & Scheffler, K. (2013). FUBAR: a fast, unconstrained bayesian approximation for inferring selection. Molecular biology and evolution30(5), 1196-1205.
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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